please help me a little

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please help me a little

Ding, Yuan Chun
Hi R Users,

I am very frustrated with the following code. Please do me a favor to run it.

after reading into the test data set (I also pasted the data set below), the first line of code for "res_coxphf" did not work and generated the error code below. but the other three line worked well.   the second line for "res_coxphf2" should be the same as the first line; I need to run more than 100 variables in a loop, so I want to do test[, i], that is why I want to use the first line.

however, the fourth line for "res_coxphf_cnaRate " also worked well after I added one variable "cna.rate" to first line. Can you run them and tell me why the first line does not run correctly?

please install coxphf package if you do not have it installed.

Thank you very much!!!

Ding

test<-read.csv("data_coxphf.csv", head=T)
res_coxphf <- coxphf(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~test[, 6], data=test)
res_coxphf2 <- coxphf(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ test$FAM138A.chr1, data=test)

res_coxph <- coxph(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ test[, 6], data=test)
res_coxphf_cnaRate <- coxphf(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ test[, 6]+ cna.rate, data=test)


> test<-read.csv("data_coxphf.csv", head=T)
> res_coxphf <- coxphf(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ test[, 6], data=test)
Error in mm1[, !colInter, drop = FALSE] :
  (subscript) logical subscript too long
> res_coxph <- coxph(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ test[, 6], data=test)
> res_coxphf_cnaRate <- coxphf(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ test[, 6]+ cna.rate, data=test)
> res_coxphf2 <- coxphf(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ test$FAM138A.chr1, data=test)
>



id      cna.rate        RFS_days2       OV_Had_a_Recurrence_CODE        DDX11L1.chr1    FAM138A.chr1    FAM138F.chr1
sn1     150     560     1       0       0       0
sn10    216     581     1       0       0       0
sn11    191     455     1       0       0       0
sn12    135     118     1       0       0       0
sn13    199     2550    0       0       0       0
sn14    312     477     1       0       0       0
sn15    260     216     1       0       0       0
sn16    400     1056    1       0       0       0
sn17    350     398     1       1       1       1
sn18    324     583     1       0       0       0
sn19    174     136     1       0       0       0
sn20    262     98      1       0       0       0
sn21    172     516     1       0       0       0
sn22    490     1439    1       0       0       0
sn23    165     365     1       0       0       0
sn24    185     168     1       0       0       0
sn25    396     1663    1       0       0       0
sn26    240     299     1       0       0       0
sn27    114     2917    0       0       0       0
sn28    128     50      1       0       0       0
sn29    190     654     1       0       0       0
sn3     435     429     1       0       0       0
sn30    268     31      1       0       0       0
sn31    175     3407    0       0       0       0
sn32    248     277     1       0       0       0
sn33    116     306     1       0       0       0
sn34    122     52      1       0       0       0
sn35    222     77      1       0       0       0
sn36    414     242     1       0       0       0
sn37    300     1034    1       1       1       1
sn38    268     3298    0       0       0       0
sn4     556     2424    0       0       0       0
sn40    274     201     1       0       0       0
sn41    267     268     1       0       0       0
sn42    325     147     1       0       0       0
sn43    323     2611    0       0       0       0
sn44    115     573     1       0       0       0
sn45    265     215     1       0       0       0
sn48    129     259     1       0       0       0
sn5     114     183     1       0       0       0
sn51    183     219     1       0       0       0
sn52    314     271     1       0       0       0
sn53    465     2071    0       0       0       0
sn54    207     44      1       0       0       0
sn55    321     347     1       0       0       0
sn56    217     1257    0       0       0       0
sn57    209     262     1       0       0       0
sn58    227     1811    0       0       0       0
sn59    130     463     1       0       0       0
sn6     320     306     1       0       0       0
sn60    136     456     1       0       0       0
sn62    208     48      1       0       0       0
sn63    253     452     1       0       0       0
sn64    326     282     1       0       0       0
sn67    260     229     1       0       0       0
sn68    329     661     0       0       0       0
sn69    478     44      1       0       0       0
sn7     263     582     1       0       0       0
sn70    309     741     1       0       0       0
sn8     223     1070    0       0       0       0
sn9     211     216     1       0       0       0


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Re: please help me a little

Jeff Newmiller
I don't use coxphf, but it is generally a bad idea to reference variables via multiple environments (e.g. global and the data= argument in this case) directly from within a formula. Just use FAM138A.chr wherever you have used test[,6] and it should work.
--
Sent from my phone. Please excuse my brevity.

On February 9, 2018 8:43:03 PM PST, "Ding, Yuan Chun" <[hidden email]> wrote:

>Hi R Users,
>
>I am very frustrated with the following code. Please do me a favor to
>run it.
>
>after reading into the test data set (I also pasted the data set
>below), the first line of code for "res_coxphf" did not work and
>generated the error code below. but the other three line worked well.  
>the second line for "res_coxphf2" should be the same as the first line;
>I need to run more than 100 variables in a loop, so I want to do test[,
>i], that is why I want to use the first line.
>
>however, the fourth line for "res_coxphf_cnaRate " also worked well
>after I added one variable "cna.rate" to first line. Can you run them
>and tell me why the first line does not run correctly?
>
>please install coxphf package if you do not have it installed.
>
>Thank you very much!!!
>
>Ding
>
>test<-read.csv("data_coxphf.csv", head=T)
>res_coxphf <- coxphf(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE)
>~test[, 6], data=test)
>res_coxphf2 <- coxphf(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE)
>~ test$FAM138A.chr1, data=test)
>
>res_coxph <- coxph(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~
>test[, 6], data=test)
>res_coxphf_cnaRate <- coxphf(formula=Surv(RFS_days2,
>OV_Had_a_Recurrence_CODE) ~ test[, 6]+ cna.rate, data=test)
>
>
>> test<-read.csv("data_coxphf.csv", head=T)
>> res_coxphf <- coxphf(formula=Surv(RFS_days2,
>OV_Had_a_Recurrence_CODE) ~ test[, 6], data=test)
>Error in mm1[, !colInter, drop = FALSE] :
>  (subscript) logical subscript too long
>> res_coxph <- coxph(formula=Surv(RFS_days2, OV_Had_a_Recurrence_CODE)
>~ test[, 6], data=test)
>> res_coxphf_cnaRate <- coxphf(formula=Surv(RFS_days2,
>OV_Had_a_Recurrence_CODE) ~ test[, 6]+ cna.rate, data=test)
>> res_coxphf2 <- coxphf(formula=Surv(RFS_days2,
>OV_Had_a_Recurrence_CODE) ~ test$FAM138A.chr1, data=test)
>>
>
>
>
>id      cna.rate        RFS_days2       OV_Had_a_Recurrence_CODE      
>DDX11L1.chr1    FAM138A.chr1    FAM138F.chr1
>sn1     150     560     1       0       0       0
>sn10    216     581     1       0       0       0
>sn11    191     455     1       0       0       0
>sn12    135     118     1       0       0       0
>sn13    199     2550    0       0       0       0
>sn14    312     477     1       0       0       0
>sn15    260     216     1       0       0       0
>sn16    400     1056    1       0       0       0
>sn17    350     398     1       1       1       1
>sn18    324     583     1       0       0       0
>sn19    174     136     1       0       0       0
>sn20    262     98      1       0       0       0
>sn21    172     516     1       0       0       0
>sn22    490     1439    1       0       0       0
>sn23    165     365     1       0       0       0
>sn24    185     168     1       0       0       0
>sn25    396     1663    1       0       0       0
>sn26    240     299     1       0       0       0
>sn27    114     2917    0       0       0       0
>sn28    128     50      1       0       0       0
>sn29    190     654     1       0       0       0
>sn3     435     429     1       0       0       0
>sn30    268     31      1       0       0       0
>sn31    175     3407    0       0       0       0
>sn32    248     277     1       0       0       0
>sn33    116     306     1       0       0       0
>sn34    122     52      1       0       0       0
>sn35    222     77      1       0       0       0
>sn36    414     242     1       0       0       0
>sn37    300     1034    1       1       1       1
>sn38    268     3298    0       0       0       0
>sn4     556     2424    0       0       0       0
>sn40    274     201     1       0       0       0
>sn41    267     268     1       0       0       0
>sn42    325     147     1       0       0       0
>sn43    323     2611    0       0       0       0
>sn44    115     573     1       0       0       0
>sn45    265     215     1       0       0       0
>sn48    129     259     1       0       0       0
>sn5     114     183     1       0       0       0
>sn51    183     219     1       0       0       0
>sn52    314     271     1       0       0       0
>sn53    465     2071    0       0       0       0
>sn54    207     44      1       0       0       0
>sn55    321     347     1       0       0       0
>sn56    217     1257    0       0       0       0
>sn57    209     262     1       0       0       0
>sn58    227     1811    0       0       0       0
>sn59    130     463     1       0       0       0
>sn6     320     306     1       0       0       0
>sn60    136     456     1       0       0       0
>sn62    208     48      1       0       0       0
>sn63    253     452     1       0       0       0
>sn64    326     282     1       0       0       0
>sn67    260     229     1       0       0       0
>sn68    329     661     0       0       0       0
>sn69    478     44      1       0       0       0
>sn7     263     582     1       0       0       0
>sn70    309     741     1       0       0       0
>sn8     223     1070    0       0       0       0
>sn9     211     216     1       0       0       0
>
>
>---------------------------------------------------------------------
>-SECURITY/CONFIDENTIALITY WARNING-
>This message (and any attachments) are intended solely ...{{dropped:28}}

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