[R] please help me a little
Ding, Yuan Chun
ycding at coh.org
Sat Feb 10 05:43:03 CET 2018
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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