Question: Problem importing 5C data
0
4.5 years ago by
gugpuccio10
Finland
gugpuccio10 wrote:

Dear All

I'm sorry if this question was answered other times, and if it's a stupid one, but i can't understand how to use the search bar in this site. Every time i look for a word it gives out empy search.

The problem:

I'm trying to import a 5C matrix with the HiTC package in R, but i'm unable to do it. This is the line of code i used:

M=importC(con = "./Desktop/ENR-HeLa-R2.csv", xgi.bed = "./Desktop/ENr.hg19.reverses", ygi.bed = "./Desktop/ENr.hg19.forwards")

And the error message is:

Genomic intervals loaded
Error in HTClist(unlist(obj)) :
all elements in '...' must be HTCexp objects
In mclapply(chromPair, function(chr) { :
all scheduled cores encountered errors in user code

Then i tried to follow the import tutorial on the HiTC manual, trying to export and then re-importing the data:

E14.bin<-binningC(E14\$chrXchrX)
exportC(E14.bin, file="E14")
importC(con="E14.mat", xgi.bed ="E14_xgi.bed", ygi.bed ="E14_ygi.bed")


Getting this error:

Genomic intervals loaded
Error in isN0(as(m, "matrix")) :
(list) object cannot be coerced to type 'double'

in this case i used "E14.mat" instead of "E14.count" as written in the tutorial, because it was the only output of the export function, together with the .bed files.

I don't understand what i'm doing wrong. I'm sorry if my question looks stupid, but i'm a newbie in R programming.


hitc importing • 595 views