chromoMap Error: .rowNamesDF<-`(x, value = value) : invalid 'row.names' length
0
0
Entering edit mode
6 weeks ago
kamanovae ▴ 50

Hi!

I am trying to run the program chromoMap. But I am getting the error:

Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length

My program start looks like this:

library(chromoMap)


chr_file_1 =read.table("~/chr_file.txt",sep = "\t", quote="", stringsAsFactors=FALSE)
print(chr_file_1)
annot_file_1= read.table("~/annotation_pos.txt",sep = "\t",quote="", stringsAsFactors=FALSE)
print(annot_file_1)

chromoMap( "chr_file.txt", "annotation_pos.txt")

All input files were generated based on the instruction

chr_file.txt:

    V1       V2       V3  
1 chr1    332315086     32400268

annot_file_1:

          V1    V2       V3       V4         V5

1    rs144848 chr13 32906729 32906729  c.1114A>C

2    rs169547 chr13 32929387 32929387  c.7397T>C

3  rs11571833 chr13 32972626 32972626  c.9976A>T

If I run the function differently, then I get a new error

chromoMap(chr_file_1, annot_file_1)

Error: The number of data files(s) must same as the number of chromsome file(s) Error in chromoMap(chr_file_1, annot_file_1) :

chromoMap R • 215 views
ADD COMMENT
0
Entering edit mode

Heys! Did you solve it? I also had a lot of issues because of formatting. Could be that the annot_file_1 is not separated by tabs? Just in case I leave here these two files that work for me:

as chr_file_1:

chr1    1   1000
chr2    1   700

and as annotation_pos:

An1 chr1    558 560
An2 chr2    396 398

I hope it helps!

ADD REPLY

Login before adding your answer.

Traffic: 1723 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