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" <ycd...@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
>
>
>---------------------------------------------------------------------
>-SECURITY/CONFIDENTIALITY WARNING-
>This message (and any attachments) are intended solely ...{{dropped:28}}
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