remove quotes from matrix

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remove quotes from matrix

greg holly
Hi all;

I have data at 734*22 dimensions with rows and columns names are
non-numeric.When I convert this data into matrix then all values show up
with quotes. Then when I use
x1= noquotes(x) to remove the quotes from the matrix then non-numeric row
names remain all other values in matrix disappear.

Your help is greatly appreciated.

Greg

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Re: remove quotes from matrix

Duncan Murdoch-2
On 19/09/2017 9:47 AM, greg holly wrote:

> Hi all;
>
> I have data at 734*22 dimensions with rows and columns names are
> non-numeric.When I convert this data into matrix then all values show up
> with quotes. Then when I use
> x1= noquotes(x) to remove the quotes from the matrix then non-numeric row
> names remain all other values in matrix disappear.
>
> Your help is greatly appreciated.
>


Matrices in R can have only one type.  If you start with a dataframe and
any columns contain character data, all entries will be converted to
character, and the matrix will be displayed with quotes.

When you say all values disappear, it sounds as though you are
displaying strings containing nothing (or just blanks).  Those will be
displayed as "" normally, but if the matrix is marked to display without
quotes, they are displayed as empty strings, so it will appear that
nothing is displayed.

You can see the structure of the original data using the str() function,
e.g. str(x) should display types for each column.

If this isn't enough to explain what's going on, please show us more
detail.  For example, show us the result of

y <- x[1:5, 1:5]
dput(y)

both before and after converting x to a matrix.

Duncan Murdoch

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Re: remove quotes from matrix

greg holly
Hi Duncan and Bert;

I do appreciate for your replies. I just figured out that after x1=
noquotes(x) commend my 733*22 matrix returns into n*1 vector. Is there way
to keep this as matrix with the dimension of 733*22?

Regards,

Greg


On Tue, Sep 19, 2017 at 10:04 AM, Duncan Murdoch <[hidden email]>
wrote:

> On 19/09/2017 9:47 AM, greg holly wrote:
>
>> Hi all;
>>
>> I have data at 734*22 dimensions with rows and columns names are
>> non-numeric.When I convert this data into matrix then all values show up
>> with quotes. Then when I use
>> x1= noquotes(x) to remove the quotes from the matrix then non-numeric row
>> names remain all other values in matrix disappear.
>>
>> Your help is greatly appreciated.
>>
>>
>
> Matrices in R can have only one type.  If you start with a dataframe and
> any columns contain character data, all entries will be converted to
> character, and the matrix will be displayed with quotes.
>
> When you say all values disappear, it sounds as though you are displaying
> strings containing nothing (or just blanks).  Those will be displayed as ""
> normally, but if the matrix is marked to display without quotes, they are
> displayed as empty strings, so it will appear that nothing is displayed.
>
> You can see the structure of the original data using the str() function,
> e.g. str(x) should display types for each column.
>
> If this isn't enough to explain what's going on, please show us more
> detail.  For example, show us the result of
>
> y <- x[1:5, 1:5]
> dput(y)
>
> both before and after converting x to a matrix.
>
> Duncan Murdoch
>

        [[alternative HTML version deleted]]

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Re: remove quotes from matrix

jdnewmil-2
Greg, I think you should stop using noquote, because it is doing something that will not be useful to you for preparing your data for analysis.

Please follow Duncan's advice and provide us with a sample of your data.  Also, please set your email program to send plain text rather than HTML formatted text.
--
Sent from my phone. Please excuse my brevity.

On September 19, 2017 7:49:12 AM PDT, greg holly <[hidden email]> wrote:

>Hi Duncan and Bert;
>
>I do appreciate for your replies. I just figured out that after x1=
>noquotes(x) commend my 733*22 matrix returns into n*1 vector. Is there
>way
>to keep this as matrix with the dimension of 733*22?
>
>Regards,
>
>Greg
>
>
>On Tue, Sep 19, 2017 at 10:04 AM, Duncan Murdoch
><[hidden email]>
>wrote:
>
>> On 19/09/2017 9:47 AM, greg holly wrote:
>>
>>> Hi all;
>>>
>>> I have data at 734*22 dimensions with rows and columns names are
>>> non-numeric.When I convert this data into matrix then all values
>show up
>>> with quotes. Then when I use
>>> x1= noquotes(x) to remove the quotes from the matrix then
>non-numeric row
>>> names remain all other values in matrix disappear.
>>>
>>> Your help is greatly appreciated.
>>>
>>>
>>
>> Matrices in R can have only one type.  If you start with a dataframe
>and
>> any columns contain character data, all entries will be converted to
>> character, and the matrix will be displayed with quotes.
>>
>> When you say all values disappear, it sounds as though you are
>displaying
>> strings containing nothing (or just blanks).  Those will be displayed
>as ""
>> normally, but if the matrix is marked to display without quotes, they
>are
>> displayed as empty strings, so it will appear that nothing is
>displayed.
>>
>> You can see the structure of the original data using the str()
>function,
>> e.g. str(x) should display types for each column.
>>
>> If this isn't enough to explain what's going on, please show us more
>> detail.  For example, show us the result of
>>
>> y <- x[1:5, 1:5]
>> dput(y)
>>
>> both before and after converting x to a matrix.
>>
>> Duncan Murdoch
>>
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

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Re: remove quotes from matrix

Bert Gunter-2
In reply to this post by greg holly
Your  claims are false -- or at least confused.

> d <- data.frame(a = I(letters[1:3]), b = 1:3)
## the I() is to prevent automatic conversion to factor

> d
  a b
1 a 1
2 b 2
3 c 3
> dm <- as.matrix(d)
> dm
     a   b
[1,] "a" "1"
[2,] "b" "2"
[3,] "c" "3"
> dimnames(dm)
[[1]]
NULL

[[2]]
[1] "a" "b"

## Note that there are no rownames, as d had none.
> dm <- noquote(dm)
> dm
     a b
[1,] a 1
[2,] b 2
[3,] c 3

We still need a reprex to resolve the confusion.

-- Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Tue, Sep 19, 2017 at 7:49 AM, greg holly <[hidden email]> wrote:

> Hi Duncan and Bert;
>
> I do appreciate for your replies. I just figured out that after x1=
> noquotes(x) commend my 733*22 matrix returns into n*1 vector. Is there way
> to keep this as matrix with the dimension of 733*22?
>
> Regards,
>
> Greg
>
>
> On Tue, Sep 19, 2017 at 10:04 AM, Duncan Murdoch <[hidden email]
> >
> wrote:
>
> > On 19/09/2017 9:47 AM, greg holly wrote:
> >
> >> Hi all;
> >>
> >> I have data at 734*22 dimensions with rows and columns names are
> >> non-numeric.When I convert this data into matrix then all values show up
> >> with quotes. Then when I use
> >> x1= noquotes(x) to remove the quotes from the matrix then non-numeric
> row
> >> names remain all other values in matrix disappear.
> >>
> >> Your help is greatly appreciated.
> >>
> >>
> >
> > Matrices in R can have only one type.  If you start with a dataframe and
> > any columns contain character data, all entries will be converted to
> > character, and the matrix will be displayed with quotes.
> >
> > When you say all values disappear, it sounds as though you are displaying
> > strings containing nothing (or just blanks).  Those will be displayed as
> ""
> > normally, but if the matrix is marked to display without quotes, they are
> > displayed as empty strings, so it will appear that nothing is displayed.
> >
> > You can see the structure of the original data using the str() function,
> > e.g. str(x) should display types for each column.
> >
> > If this isn't enough to explain what's going on, please show us more
> > detail.  For example, show us the result of
> >
> > y <- x[1:5, 1:5]
> > dput(y)
> >
> > both before and after converting x to a matrix.
> >
> > Duncan Murdoch
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

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Re: remove quotes from matrix

greg holly
In reply to this post by Duncan Murdoch-2
Dear all;

Thanks. Here are the dput results as Duncan suggested.

Regards,

Greg

structure(list(Sub_Pathways = structure(c(3L, 3L, 3L, 3L, 3L), .Label =
c("Acetylated_Peptides",
"Advanced_Glycation_End-product", "Alanine_and_Aspartate", "Aminosugar",
"Ascorbate_and_Aldarate", "Carnitine", "Ceramides", "Creatine",
"Diacylglycerol", "Dipeptide", "Dipeptide_Derivative",
"Disaccharides_and_Oligosaccharides",
"Eicosanoid", "Endocannabinoid", "Fatty_Acid(Acyl_Carnitine)",
"Fatty_Acid(Acyl_Glycine)", "Fatty_Acid,_Amino", "Fatty_Acid,_Branched",
"Fatty_Acid,_Dicarboxylate", "Fatty_Acid,_Dihydroxy",
"Fatty_Acid,_Monohydroxy",
"Fatty_Acid_(Acyl_Choline)", "Fatty_Acid_(Acyl_Glutamine)",
"Fatty_Acid_(also_BCAA)",
"Fatty_Acid_Synthesis", "Fibrinogen_Cleavage_Peptide",
"Fructose,_Mannose_and_Galactose",
"Gamma-glutamyl_Amino_Acid", "Glutamate", "Glutathione", "Glycerolipid",
"Glycine,_Serine_and_Threonine", "Glycogen",
"Glycolysis,_Gluconeogenesis,_and_Pyruvate",
"Guanidino_and_Acetamido", "Hemoglobin_and_Porphyrin", "Histidine",
"Inositol", "Ketone_Bodies", "Leucine,_Isoleucine_and_Valine",
"Long_Chain_Fatty_Acid", "Lysine", "Lyso-phospho-ether", "Lysolipid",
"Lysoplasmalogen", "Medium_Chain_Fatty_Acid",
"Methionine,_Cysteine,_SAM_and_Taurine",
"Mevalonate", "Monoacylglycerol", "Nicotinate_and_Nicotinamide",
"Oxidative_Phosphorylation", "Pantothenate_and_CoA", "Pentose",
"Phenylalanine_and_Tyrosine", "Phospholipid", "Plasmalogen",
"Polyamine", "Polypeptide", "Polyunsaturated_Fatty_Acid_(n3_and_n6)",
"Primary_Bile_Acid", "Purine,_(Hypo)Xanthine/Inosine_containing",
"Purine,_Adenine_containing", "Purine,_Guanine_containing",
"Pyrimidine,_Cytidine_containing",
"Pyrimidine,_Orotate_containing", "Pyrimidine,_Thymine_containing",
"Pyrimidine,_Uracil_containing", "Riboflavin", "Secondary_Bile_Acid",
"Short_Chain_Fatty_Acid", "Sphingolipid", "Steroid", "Sterol",
"TCA_Cycle", "Tocopherol", "Tryptophan",
"Urea_cycle;_Arginine_and_Proline",
"Vitamin_A", "Vitamin_B6"), class = "factor"), BMI_beta = c(0.2382,
-0.313, 0.1238, 0.3035, -0.00982), SAT_beta = c(-0.02409, -1.9751,
0.4095, 0.4861, 0.3293), VAT_beta = c(0.9418, -2.2204, 0.6805,
0.7083, 0.01597), VSR_beta = c(0.2469, -0.2354, 0.05539, 0.01337,
-0.04353)), .Names = c("Sub_Pathways", "BMI_beta", "SAT_beta",
"VAT_beta", "VSR_beta"), row.names = c(NA, 5L), class = "data.frame")

On Tue, Sep 19, 2017 at 10:04 AM, Duncan Murdoch <[hidden email]>
wrote:

> On 19/09/2017 9:47 AM, greg holly wrote:
>
>> Hi all;
>>
>> I have data at 734*22 dimensions with rows and columns names are
>> non-numeric.When I convert this data into matrix then all values show up
>> with quotes. Then when I use
>> x1= noquotes(x) to remove the quotes from the matrix then non-numeric row
>> names remain all other values in matrix disappear.
>>
>> Your help is greatly appreciated.
>>
>>
>
> Matrices in R can have only one type.  If you start with a dataframe and
> any columns contain character data, all entries will be converted to
> character, and the matrix will be displayed with quotes.
>
> When you say all values disappear, it sounds as though you are displaying
> strings containing nothing (or just blanks).  Those will be displayed as ""
> normally, but if the matrix is marked to display without quotes, they are
> displayed as empty strings, so it will appear that nothing is displayed.
>
> You can see the structure of the original data using the str() function,
> e.g. str(x) should display types for each column.
>
> If this isn't enough to explain what's going on, please show us more
> detail.  For example, show us the result of
>
> y <- x[1:5, 1:5]
> dput(y)
>
> both before and after converting x to a matrix.
>
> Duncan Murdoch
>

        [[alternative HTML version deleted]]

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Re: remove quotes from matrix

Bert Gunter-2
Works fine for me. What do you object to in the following?

Calling the above df "d",

> dm <- as.matrix(d)
> dm
  Sub_Pathways            BMI_beta   SAT_beta   VAT_beta
1 "Alanine_and_Aspartate" " 0.23820" "-0.02409" " 0.94180"
2 "Alanine_and_Aspartate" "-0.31300" "-1.97510" "-2.22040"
3 "Alanine_and_Aspartate" " 0.12380" " 0.40950" " 0.68050"
4 "Alanine_and_Aspartate" " 0.30350" " 0.48610" " 0.70830"
5 "Alanine_and_Aspartate" "-0.00982" " 0.32930" " 0.01597"
  VSR_beta
1 " 0.24690"
2 "-0.23540"
3 " 0.05539"
4 " 0.01337"
5 "-0.04353"
> dimnames(dm)
[[1]]
[1] "1" "2" "3" "4" "5"

[[2]]
[1] "Sub_Pathways" "BMI_beta"     "SAT_beta"     "VAT_beta"
[5] "VSR_beta"

> dm <- noquote(dm)
> dm
  Sub_Pathways          BMI_beta SAT_beta VAT_beta VSR_beta
1 Alanine_and_Aspartate  0.23820 -0.02409  0.94180  0.24690
2 Alanine_and_Aspartate -0.31300 -1.97510 -2.22040 -0.23540
3 Alanine_and_Aspartate  0.12380  0.40950  0.68050  0.05539
4 Alanine_and_Aspartate  0.30350  0.48610  0.70830  0.01337
5 Alanine_and_Aspartate -0.00982  0.32930  0.01597 -0.04353
> dimnames(dm)
[[1]]
[1] "1" "2" "3" "4" "5"

[[2]]
[1] "Sub_Pathways" "BMI_beta"     "SAT_beta"     "VAT_beta"
[5] "VSR_beta"


Perhaps you need to read ?noquote or ?matrix.

-- Bert



Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Tue, Sep 19, 2017 at 8:20 AM, greg holly <[hidden email]> wrote:

> Dear all;
>
> Thanks. Here are the dput results as Duncan suggested.
>
> Regards,
>
> Greg
>
> structure(list(Sub_Pathways = structure(c(3L, 3L, 3L, 3L, 3L), .Label =
> c("Acetylated_Peptides",
> "Advanced_Glycation_End-product", "Alanine_and_Aspartate", "Aminosugar",
> "Ascorbate_and_Aldarate", "Carnitine", "Ceramides", "Creatine",
> "Diacylglycerol", "Dipeptide", "Dipeptide_Derivative",
> "Disaccharides_and_Oligosaccharides",
> "Eicosanoid", "Endocannabinoid", "Fatty_Acid(Acyl_Carnitine)",
> "Fatty_Acid(Acyl_Glycine)", "Fatty_Acid,_Amino", "Fatty_Acid,_Branched",
> "Fatty_Acid,_Dicarboxylate", "Fatty_Acid,_Dihydroxy",
> "Fatty_Acid,_Monohydroxy",
> "Fatty_Acid_(Acyl_Choline)", "Fatty_Acid_(Acyl_Glutamine)",
> "Fatty_Acid_(also_BCAA)",
> "Fatty_Acid_Synthesis", "Fibrinogen_Cleavage_Peptide",
> "Fructose,_Mannose_and_Galactose",
> "Gamma-glutamyl_Amino_Acid", "Glutamate", "Glutathione", "Glycerolipid",
> "Glycine,_Serine_and_Threonine", "Glycogen",
> "Glycolysis,_Gluconeogenesis,_and_Pyruvate",
> "Guanidino_and_Acetamido", "Hemoglobin_and_Porphyrin", "Histidine",
> "Inositol", "Ketone_Bodies", "Leucine,_Isoleucine_and_Valine",
> "Long_Chain_Fatty_Acid", "Lysine", "Lyso-phospho-ether", "Lysolipid",
> "Lysoplasmalogen", "Medium_Chain_Fatty_Acid",
> "Methionine,_Cysteine,_SAM_and_Taurine",
> "Mevalonate", "Monoacylglycerol", "Nicotinate_and_Nicotinamide",
> "Oxidative_Phosphorylation", "Pantothenate_and_CoA", "Pentose",
> "Phenylalanine_and_Tyrosine", "Phospholipid", "Plasmalogen",
> "Polyamine", "Polypeptide", "Polyunsaturated_Fatty_Acid_(n3_and_n6)",
> "Primary_Bile_Acid", "Purine,_(Hypo)Xanthine/Inosine_containing",
> "Purine,_Adenine_containing", "Purine,_Guanine_containing",
> "Pyrimidine,_Cytidine_containing",
> "Pyrimidine,_Orotate_containing", "Pyrimidine,_Thymine_containing",
> "Pyrimidine,_Uracil_containing", "Riboflavin", "Secondary_Bile_Acid",
> "Short_Chain_Fatty_Acid", "Sphingolipid", "Steroid", "Sterol",
> "TCA_Cycle", "Tocopherol", "Tryptophan",
> "Urea_cycle;_Arginine_and_Proline",
> "Vitamin_A", "Vitamin_B6"), class = "factor"), BMI_beta = c(0.2382,
> -0.313, 0.1238, 0.3035, -0.00982), SAT_beta = c(-0.02409, -1.9751,
> 0.4095, 0.4861, 0.3293), VAT_beta = c(0.9418, -2.2204, 0.6805,
> 0.7083, 0.01597), VSR_beta = c(0.2469, -0.2354, 0.05539, 0.01337,
> -0.04353)), .Names = c("Sub_Pathways", "BMI_beta", "SAT_beta",
> "VAT_beta", "VSR_beta"), row.names = c(NA, 5L), class = "data.frame")
>
> On Tue, Sep 19, 2017 at 10:04 AM, Duncan Murdoch <[hidden email]
> >
> wrote:
>
> > On 19/09/2017 9:47 AM, greg holly wrote:
> >
> >> Hi all;
> >>
> >> I have data at 734*22 dimensions with rows and columns names are
> >> non-numeric.When I convert this data into matrix then all values show up
> >> with quotes. Then when I use
> >> x1= noquotes(x) to remove the quotes from the matrix then non-numeric
> row
> >> names remain all other values in matrix disappear.
> >>
> >> Your help is greatly appreciated.
> >>
> >>
> >
> > Matrices in R can have only one type.  If you start with a dataframe and
> > any columns contain character data, all entries will be converted to
> > character, and the matrix will be displayed with quotes.
> >
> > When you say all values disappear, it sounds as though you are displaying
> > strings containing nothing (or just blanks).  Those will be displayed as
> ""
> > normally, but if the matrix is marked to display without quotes, they are
> > displayed as empty strings, so it will appear that nothing is displayed.
> >
> > You can see the structure of the original data using the str() function,
> > e.g. str(x) should display types for each column.
> >
> > If this isn't enough to explain what's going on, please show us more
> > detail.  For example, show us the result of
> >
> > y <- x[1:5, 1:5]
> > dput(y)
> >
> > both before and after converting x to a matrix.
> >
> > Duncan Murdoch
> >
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

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Re: remove quotes from matrix

David Carlson
In reply to this post by greg holly
Your description was confusing. You do not have row names that are non-numeric:

> str(dta)
'data.frame':   5 obs. of  5 variables:
 $ Sub_Pathways: Factor w/ 79 levels "Acetylated_Peptides",..: 3 3 3 3 3
 $ BMI_beta    : num  0.2382 -0.313 0.1238 0.3035 -0.00982
 $ SAT_beta    : num  -0.0241 -1.9751 0.4095 0.4861 0.3293
 $ VAT_beta    : num  0.942 -2.22 0.68 0.708 0.016
 $ VSR_beta    : num  0.2469 -0.2354 0.0554 0.0134 -0.0435

You have a column that is a factor with 79 levels. That cannot be row names because you indicated that the original data was 734*22 dimensions and row names cannot have duplications. If you want numeric values, you need to strip off the first column:

> as.matrix(dta[ , -1])
  BMI_beta SAT_beta VAT_beta VSR_beta
1  0.23820 -0.02409  0.94180  0.24690
2 -0.31300 -1.97510 -2.22040 -0.23540
3  0.12380  0.40950  0.68050  0.05539
4  0.30350  0.48610  0.70830  0.01337
5 -0.00982  0.32930  0.01597 -0.04353

If you just want to print the character values without quotes:

> print(as.matrix(dta), quote=FALSE)
  Sub_Pathways          BMI_beta SAT_beta VAT_beta VSR_beta
1 Alanine_and_Aspartate  0.23820 -0.02409  0.94180  0.24690
2 Alanine_and_Aspartate -0.31300 -1.97510 -2.22040 -0.23540
3 Alanine_and_Aspartate  0.12380  0.40950  0.68050  0.05539
4 Alanine_and_Aspartate  0.30350  0.48610  0.70830  0.01337
5 Alanine_and_Aspartate -0.00982  0.32930  0.01597 -0.04353

But do not forget that they are still character strings.

----------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77843-4352



-----Original Message-----
From: R-help [mailto:[hidden email]] On Behalf Of greg holly
Sent: Tuesday, September 19, 2017 10:21 AM
To: Duncan Murdoch <[hidden email]>
Cc: r-help mailing list <[hidden email]>
Subject: Re: [R] remove quotes from matrix

Dear all;

Thanks. Here are the dput results as Duncan suggested.

Regards,

Greg

structure(list(Sub_Pathways = structure(c(3L, 3L, 3L, 3L, 3L), .Label = c("Acetylated_Peptides", "Advanced_Glycation_End-product", "Alanine_and_Aspartate", "Aminosugar", "Ascorbate_and_Aldarate", "Carnitine", "Ceramides", "Creatine", "Diacylglycerol", "Dipeptide", "Dipeptide_Derivative", "Disaccharides_and_Oligosaccharides",
"Eicosanoid", "Endocannabinoid", "Fatty_Acid(Acyl_Carnitine)", "Fatty_Acid(Acyl_Glycine)", "Fatty_Acid,_Amino", "Fatty_Acid,_Branched", "Fatty_Acid,_Dicarboxylate", "Fatty_Acid,_Dihydroxy", "Fatty_Acid,_Monohydroxy", "Fatty_Acid_(Acyl_Choline)", "Fatty_Acid_(Acyl_Glutamine)", "Fatty_Acid_(also_BCAA)", "Fatty_Acid_Synthesis", "Fibrinogen_Cleavage_Peptide", "Fructose,_Mannose_and_Galactose",
"Gamma-glutamyl_Amino_Acid", "Glutamate", "Glutathione", "Glycerolipid", "Glycine,_Serine_and_Threonine", "Glycogen", "Glycolysis,_Gluconeogenesis,_and_Pyruvate",
"Guanidino_and_Acetamido", "Hemoglobin_and_Porphyrin", "Histidine", "Inositol", "Ketone_Bodies", "Leucine,_Isoleucine_and_Valine", "Long_Chain_Fatty_Acid", "Lysine", "Lyso-phospho-ether", "Lysolipid", "Lysoplasmalogen", "Medium_Chain_Fatty_Acid", "Methionine,_Cysteine,_SAM_and_Taurine",
"Mevalonate", "Monoacylglycerol", "Nicotinate_and_Nicotinamide", "Oxidative_Phosphorylation", "Pantothenate_and_CoA", "Pentose", "Phenylalanine_and_Tyrosine", "Phospholipid", "Plasmalogen", "Polyamine", "Polypeptide", "Polyunsaturated_Fatty_Acid_(n3_and_n6)",
"Primary_Bile_Acid", "Purine,_(Hypo)Xanthine/Inosine_containing",
"Purine,_Adenine_containing", "Purine,_Guanine_containing", "Pyrimidine,_Cytidine_containing",
"Pyrimidine,_Orotate_containing", "Pyrimidine,_Thymine_containing", "Pyrimidine,_Uracil_containing", "Riboflavin", "Secondary_Bile_Acid", "Short_Chain_Fatty_Acid", "Sphingolipid", "Steroid", "Sterol", "TCA_Cycle", "Tocopherol", "Tryptophan", "Urea_cycle;_Arginine_and_Proline",
"Vitamin_A", "Vitamin_B6"), class = "factor"), BMI_beta = c(0.2382, -0.313, 0.1238, 0.3035, -0.00982), SAT_beta = c(-0.02409, -1.9751, 0.4095, 0.4861, 0.3293), VAT_beta = c(0.9418, -2.2204, 0.6805, 0.7083, 0.01597), VSR_beta = c(0.2469, -0.2354, 0.05539, 0.01337, -0.04353)), .Names = c("Sub_Pathways", "BMI_beta", "SAT_beta", "VAT_beta", "VSR_beta"), row.names = c(NA, 5L), class = "data.frame")

On Tue, Sep 19, 2017 at 10:04 AM, Duncan Murdoch <[hidden email]>
wrote:

> On 19/09/2017 9:47 AM, greg holly wrote:
>
>> Hi all;
>>
>> I have data at 734*22 dimensions with rows and columns names are
>> non-numeric.When I convert this data into matrix then all values show
>> up with quotes. Then when I use x1= noquotes(x) to remove the quotes
>> from the matrix then non-numeric row names remain all other values in
>> matrix disappear.
>>
>> Your help is greatly appreciated.
>>
>>
>
> Matrices in R can have only one type.  If you start with a dataframe
> and any columns contain character data, all entries will be converted
> to character, and the matrix will be displayed with quotes.
>
> When you say all values disappear, it sounds as though you are
> displaying strings containing nothing (or just blanks).  Those will be displayed as ""
> normally, but if the matrix is marked to display without quotes, they
> are displayed as empty strings, so it will appear that nothing is displayed.
>
> You can see the structure of the original data using the str()
> function, e.g. str(x) should display types for each column.
>
> If this isn't enough to explain what's going on, please show us more
> detail.  For example, show us the result of
>
> y <- x[1:5, 1:5]
> dput(y)
>
> both before and after converting x to a matrix.
>
> Duncan Murdoch
>

        [[alternative HTML version deleted]]

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Re: remove quotes from matrix

greg holly
In reply to this post by Bert Gunter-2
Hi Bert;

I sincerely appreciate for this. When I follow your way I have got
dimnames(dm)
[[1]]
NULL

I think this is the reason why the matrix is being converted into  a column
vector.

Regards,

Greg

On Tue, Sep 19, 2017 at 11:32 AM, Bert Gunter <[hidden email]>
wrote:

> Works fine for me. What do you object to in the following?
>
> Calling the above df "d",
>
> > dm <- as.matrix(d)
> > dm
>   Sub_Pathways            BMI_beta   SAT_beta   VAT_beta
> 1 "Alanine_and_Aspartate" " 0.23820" "-0.02409" " 0.94180"
> 2 "Alanine_and_Aspartate" "-0.31300" "-1.97510" "-2.22040"
> 3 "Alanine_and_Aspartate" " 0.12380" " 0.40950" " 0.68050"
> 4 "Alanine_and_Aspartate" " 0.30350" " 0.48610" " 0.70830"
> 5 "Alanine_and_Aspartate" "-0.00982" " 0.32930" " 0.01597"
>   VSR_beta
> 1 " 0.24690"
> 2 "-0.23540"
> 3 " 0.05539"
> 4 " 0.01337"
> 5 "-0.04353"
> > dimnames(dm)
> [[1]]
> [1] "1" "2" "3" "4" "5"
>
> [[2]]
> [1] "Sub_Pathways" "BMI_beta"     "SAT_beta"     "VAT_beta"
> [5] "VSR_beta"
>
> > dm <- noquote(dm)
> > dm
>   Sub_Pathways          BMI_beta SAT_beta VAT_beta VSR_beta
> 1 Alanine_and_Aspartate  0.23820 -0.02409  0.94180  0.24690
> 2 Alanine_and_Aspartate -0.31300 -1.97510 -2.22040 -0.23540
> 3 Alanine_and_Aspartate  0.12380  0.40950  0.68050  0.05539
> 4 Alanine_and_Aspartate  0.30350  0.48610  0.70830  0.01337
> 5 Alanine_and_Aspartate -0.00982  0.32930  0.01597 -0.04353
> > dimnames(dm)
> [[1]]
> [1] "1" "2" "3" "4" "5"
>
> [[2]]
> [1] "Sub_Pathways" "BMI_beta"     "SAT_beta"     "VAT_beta"
> [5] "VSR_beta"
>
>
> Perhaps you need to read ?noquote or ?matrix.
>
> -- Bert
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and
> sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Tue, Sep 19, 2017 at 8:20 AM, greg holly <[hidden email]> wrote:
>
>> Dear all;
>>
>> Thanks. Here are the dput results as Duncan suggested.
>>
>> Regards,
>>
>> Greg
>>
>> structure(list(Sub_Pathways = structure(c(3L, 3L, 3L, 3L, 3L), .Label =
>> c("Acetylated_Peptides",
>> "Advanced_Glycation_End-product", "Alanine_and_Aspartate", "Aminosugar",
>> "Ascorbate_and_Aldarate", "Carnitine", "Ceramides", "Creatine",
>> "Diacylglycerol", "Dipeptide", "Dipeptide_Derivative",
>> "Disaccharides_and_Oligosaccharides",
>> "Eicosanoid", "Endocannabinoid", "Fatty_Acid(Acyl_Carnitine)",
>> "Fatty_Acid(Acyl_Glycine)", "Fatty_Acid,_Amino", "Fatty_Acid,_Branched",
>> "Fatty_Acid,_Dicarboxylate", "Fatty_Acid,_Dihydroxy",
>> "Fatty_Acid,_Monohydroxy",
>> "Fatty_Acid_(Acyl_Choline)", "Fatty_Acid_(Acyl_Glutamine)",
>> "Fatty_Acid_(also_BCAA)",
>> "Fatty_Acid_Synthesis", "Fibrinogen_Cleavage_Peptide",
>> "Fructose,_Mannose_and_Galactose",
>> "Gamma-glutamyl_Amino_Acid", "Glutamate", "Glutathione", "Glycerolipid",
>> "Glycine,_Serine_and_Threonine", "Glycogen",
>> "Glycolysis,_Gluconeogenesis,_and_Pyruvate",
>> "Guanidino_and_Acetamido", "Hemoglobin_and_Porphyrin", "Histidine",
>> "Inositol", "Ketone_Bodies", "Leucine,_Isoleucine_and_Valine",
>> "Long_Chain_Fatty_Acid", "Lysine", "Lyso-phospho-ether", "Lysolipid",
>> "Lysoplasmalogen", "Medium_Chain_Fatty_Acid",
>> "Methionine,_Cysteine,_SAM_and_Taurine",
>> "Mevalonate", "Monoacylglycerol", "Nicotinate_and_Nicotinamide",
>> "Oxidative_Phosphorylation", "Pantothenate_and_CoA", "Pentose",
>> "Phenylalanine_and_Tyrosine", "Phospholipid", "Plasmalogen",
>> "Polyamine", "Polypeptide", "Polyunsaturated_Fatty_Acid_(n3_and_n6)",
>> "Primary_Bile_Acid", "Purine,_(Hypo)Xanthine/Inosine_containing",
>> "Purine,_Adenine_containing", "Purine,_Guanine_containing",
>> "Pyrimidine,_Cytidine_containing",
>> "Pyrimidine,_Orotate_containing", "Pyrimidine,_Thymine_containing",
>> "Pyrimidine,_Uracil_containing", "Riboflavin", "Secondary_Bile_Acid",
>> "Short_Chain_Fatty_Acid", "Sphingolipid", "Steroid", "Sterol",
>> "TCA_Cycle", "Tocopherol", "Tryptophan",
>> "Urea_cycle;_Arginine_and_Proline",
>> "Vitamin_A", "Vitamin_B6"), class = "factor"), BMI_beta = c(0.2382,
>> -0.313, 0.1238, 0.3035, -0.00982), SAT_beta = c(-0.02409, -1.9751,
>> 0.4095, 0.4861, 0.3293), VAT_beta = c(0.9418, -2.2204, 0.6805,
>> 0.7083, 0.01597), VSR_beta = c(0.2469, -0.2354, 0.05539, 0.01337,
>> -0.04353)), .Names = c("Sub_Pathways", "BMI_beta", "SAT_beta",
>> "VAT_beta", "VSR_beta"), row.names = c(NA, 5L), class = "data.frame")
>>
>> On Tue, Sep 19, 2017 at 10:04 AM, Duncan Murdoch <
>> [hidden email]>
>> wrote:
>>
>> > On 19/09/2017 9:47 AM, greg holly wrote:
>> >
>> >> Hi all;
>> >>
>> >> I have data at 734*22 dimensions with rows and columns names are
>> >> non-numeric.When I convert this data into matrix then all values show
>> up
>> >> with quotes. Then when I use
>> >> x1= noquotes(x) to remove the quotes from the matrix then non-numeric
>> row
>> >> names remain all other values in matrix disappear.
>> >>
>> >> Your help is greatly appreciated.
>> >>
>> >>
>> >
>> > Matrices in R can have only one type.  If you start with a dataframe and
>> > any columns contain character data, all entries will be converted to
>> > character, and the matrix will be displayed with quotes.
>> >
>> > When you say all values disappear, it sounds as though you are
>> displaying
>> > strings containing nothing (or just blanks).  Those will be displayed
>> as ""
>> > normally, but if the matrix is marked to display without quotes, they
>> are
>> > displayed as empty strings, so it will appear that nothing is displayed.
>> >
>> > You can see the structure of the original data using the str() function,
>> > e.g. str(x) should display types for each column.
>> >
>> > If this isn't enough to explain what's going on, please show us more
>> > detail.  For example, show us the result of
>> >
>> > y <- x[1:5, 1:5]
>> > dput(y)
>> >
>> > both before and after converting x to a matrix.
>> >
>> > Duncan Murdoch
>> >
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posti
>> ng-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.