[R] please help me a little

Jeff Newmiller jdnewmil at dcn.davis.ca.us
Sat Feb 10 06:58:56 CET 2018


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" <ycding at coh.org> 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
>
>
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