exomeCopy error in col name
1
0
Entering edit mode
@chiararigobello-15139
Last seen 3.1 years ago

Hi , I'm having an error in exomeCopy when I computate fit.

(No previous error, following the vignette, and with provided data).

> fit <- exomeCopy(counts[seqnames(counts) ==
+ "chr1"], sample.name = "BIR", X.names = c("log.bg",
+ "GC", "GC.sq", "width"), S = 0:6, d = 2)
Error in exomeCopy(counts[seqnames(counts) == "chr1"], sample.name = "BIR",  :
  sample.name is not a column in rdata.

I've tried to check all objects containing name, but probably I've missed something!

 

any suggestion is appreciated

 

chiara

exomecopy • 271 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 1 hour ago
United States

Can you show that BIR is in fact a name in the mcols of the object? (That message is somewhat outdated because we no longer use RangedData but now GRanges.)

ADD COMMENT
0
Entering edit mode

I know that the problem is in that.

If I look at

colnames(mcols(counts))
 [1] "BIP"    "BIR"    "BIQ"    "AWI"    "AWJ"    "AWK"    "AWL"    "AWM"   
 [9] "BQ0"    "GC"     "GC.sq"  "bg"     "log.bg" "wdth"   "bg.var"

(That message is somewhat outdated because we no longer use RangedData but now GRanges.) --> how can I verified this?

Sorry, but I'm a self-taught in bioinformatics.

thanks for your help

 

 

ADD REPLY
0
Entering edit mode

And are you using version 1.24 (the most recent version)?

ADD REPLY

Login before adding your answer.

Traffic: 482 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6