[R] Problem with Grep Under Loop

[Gundala Viswanath]

Dear all,

I have no problem with this individual grep command:

> datk <- grep("XM_528056", source$V1)
> dat2 <- source[datk,]
> print(dat2)
             V1      V2   V3 V4      V5      V6         V7
35995 XM_528056 panTro2 chr8  + 1775569 1896107 Chimpanzee


BUT, when I run them under the loop it gives this error:


> hm_acc <- c("XM_528056","AB002296")
> for (i in 1:length(hm_acc)){
+
+    hm_acc_id <- as.character(hm_acc[i])
+    print(hm_acc_id)
+
+    hm_allk <- grep(hm_acc_id,source$V1)
+    hm_all <- source[hm_allk,]
+
+    print(hm_all)
+ }

[1] "XM_528056"
[1] V1 V2 V3 V4 V5 V6 V7
<0 rows> (or 0-length row.names)
[1] "AB002296"
[1] V1 V2 V3 V4 V5 V6 V7
<0 rows> (or 0-length row.names)
.....

What's wrong with my way of using grep?
Please advice.


- Gundala Viswanath
Jakarta - Indonesia