Question concerning Loading large Data Sets

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Question concerning Loading large Data Sets

Spencer Brackett
Good evening,

I am attempting to reproduce the following lines of code...

library(data.table)
anno = as.data.frame(fread(file = "file name", sep ="\t", header = T))


The following is my attempt...

> library(data.table)
> mapper <- read.delim("~/Vakul's GBM code/mapper.txt")
>   View(mapper)
## fread() was used as datset is quite large ##
> GBM_meth <- fread("~/Vakul's GBM code/mapper.txt")
> anno = as.data.frame(fread(file = "~/Vakul's GBM code/mapper.txt", sep
="\t", header = T))

Via View(mapper), I can view the dataset contained within the "mapper.txt"
file, but the >anno = as.data.frame portion does not trigger any sort of
'response' on R and simply brings my cursor down to the next line, ready
for further implementation. Should I be getting some sort of output from R,
and if so what should I expect?

I apologize in advance for any errors in the summary of the above script

Best,

Spencer Brackett

        [[alternative HTML version deleted]]

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Re: Question concerning Loading large Data Sets

Spencer Brackett
Also,

In case there is any confusion... "~/Vakul's GBM code" was set up in the
working directory (via setwd) as the folder in which the file 'mapper.txt'
is contained... thereby making the "~/Vakul's GBM code/mapper.txt" as
shown.

Should I perhaps reset my working directory to the file I'm trying to
access, exclusively?

On Sun, May 5, 2019 at 7:09 PM Spencer Brackett <
[hidden email]> wrote:

> Good evening,
>
> I am attempting to reproduce the following lines of code...
>
> library(data.table)
> anno = as.data.frame(fread(file = "file name", sep ="\t", header = T))
>
>
> The following is my attempt...
>
> > library(data.table)
> > mapper <- read.delim("~/Vakul's GBM code/mapper.txt")
> >   View(mapper)
> ## fread() was used as datset is quite large ##
> > GBM_meth <- fread("~/Vakul's GBM code/mapper.txt")
> > anno = as.data.frame(fread(file = "~/Vakul's GBM code/mapper.txt", sep
> ="\t", header = T))
>
> Via View(mapper), I can view the dataset contained within the "mapper.txt"
> file, but the >anno = as.data.frame portion does not trigger any sort of
> 'response' on R and simply brings my cursor down to the next line, ready
> for further implementation. Should I be getting some sort of output from R,
> and if so what should I expect?
>
> I apologize in advance for any errors in the summary of the above script
>
> Best,
>
> Spencer Brackett
>

        [[alternative HTML version deleted]]

______________________________________________
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and provide commented, minimal, self-contained, reproducible code.
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Re: Question concerning Loading large Data Sets

David Winsemius
I wouldn’t have expected an message, but it does raise the question: why are you making two different copies of the same text file if you are concerned about size issues?


David

Sent from my iPhone

> On May 5, 2019, at 5:14 PM, Spencer Brackett <[hidden email]> wrote:
>
> Also,
>
> In case there is any confusion... "~/Vakul's GBM code" was set up in the
> working directory (via setwd) as the folder in which the file 'mapper.txt'
> is contained... thereby making the "~/Vakul's GBM code/mapper.txt" as
> shown.
>
> Should I perhaps reset my working directory to the file I'm trying to
> access, exclusively?
>
> On Sun, May 5, 2019 at 7:09 PM Spencer Brackett <
> [hidden email]> wrote:
>
>> Good evening,
>>
>> I am attempting to reproduce the following lines of code...
>>
>> library(data.table)
>> anno = as.data.frame(fread(file = "file name", sep ="\t", header = T))
>>
>>
>> The following is my attempt...
>>
>>> library(data.table)
>>> mapper <- read.delim("~/Vakul's GBM code/mapper.txt")
>>>  View(mapper)
>> ## fread() was used as datset is quite large ##
>>> GBM_meth <- fread("~/Vakul's GBM code/mapper.txt")
>>> anno = as.data.frame(fread(file = "~/Vakul's GBM code/mapper.txt", sep
>> ="\t", header = T))
>>
>> Via View(mapper), I can view the dataset contained within the "mapper.txt"
>> file, but the >anno = as.data.frame portion does not trigger any sort of
>> 'response' on R and simply brings my cursor down to the next line, ready
>> for further implementation. Should I be getting some sort of output from R,
>> and if so what should I expect?
>>
>> I apologize in advance for any errors in the summary of the above script
>>
>> Best,
>>
>> Spencer Brackett
>>
>
>    [[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.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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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: Question concerning Loading large Data Sets

Eric Berger
I don't think I understand your question.
What if you enter

class(anno)

Does that give anything?


On Mon, May 6, 2019 at 2:29 AM David Winsemius <[hidden email]>
wrote:

> I wouldn’t have expected an message, but it does raise the question: why
> are you making two different copies of the same text file if you are
> concerned about size issues?
>
> —
> David
>
> Sent from my iPhone
>
> > On May 5, 2019, at 5:14 PM, Spencer Brackett <
> [hidden email]> wrote:
> >
> > Also,
> >
> > In case there is any confusion... "~/Vakul's GBM code" was set up in the
> > working directory (via setwd) as the folder in which the file
> 'mapper.txt'
> > is contained... thereby making the "~/Vakul's GBM code/mapper.txt" as
> > shown.
> >
> > Should I perhaps reset my working directory to the file I'm trying to
> > access, exclusively?
> >
> > On Sun, May 5, 2019 at 7:09 PM Spencer Brackett <
> > [hidden email]> wrote:
> >
> >> Good evening,
> >>
> >> I am attempting to reproduce the following lines of code...
> >>
> >> library(data.table)
> >> anno = as.data.frame(fread(file = "file name", sep ="\t", header = T))
> >>
> >>
> >> The following is my attempt...
> >>
> >>> library(data.table)
> >>> mapper <- read.delim("~/Vakul's GBM code/mapper.txt")
> >>>  View(mapper)
> >> ## fread() was used as datset is quite large ##
> >>> GBM_meth <- fread("~/Vakul's GBM code/mapper.txt")
> >>> anno = as.data.frame(fread(file = "~/Vakul's GBM code/mapper.txt", sep
> >> ="\t", header = T))
> >>
> >> Via View(mapper), I can view the dataset contained within the
> "mapper.txt"
> >> file, but the >anno = as.data.frame portion does not trigger any sort of
> >> 'response' on R and simply brings my cursor down to the next line, ready
> >> for further implementation. Should I be getting some sort of output
> from R,
> >> and if so what should I expect?
> >>
> >> I apologize in advance for any errors in the summary of the above script
> >>
> >> Best,
> >>
> >> Spencer Brackett
> >>
> >
> >    [[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.
>
> ______________________________________________
> [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]]

______________________________________________
[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.