Problem in createReplicTimingFile.R

[giorgiabiddau]

Hi all,

I think there's a problem with the function "createReplicTimingFile.R".
Specifically, when I run it, I get an error at line 8

8. loci_gr <- GRanges(seqnames = loci[,2], ranges = IRanges(start = loci[,3], width = 1))

If I understand correctly, "loci" should be a dataframe with two columns (chromosomes and positions).
I tried to solve it by replacing 2 with 1 and 3 with 2:

8. loci_gr <- GRanges(seqnames = loci[,1], ranges = IRanges(start = loci[,2], width = 1))

I would like to know whether the solution is appropriate!

Thank you so much in advance!

Giorgia

[tlesluyes]

Hi @giorgiabiddau,

The loci object corresponds to the SNPpos example provided here. It should be a table with 3 columns: probe IDs, chromosomes and positions. Internally, ASCAT derives the loci_gr object as follows (so the 3 columns are used):

loci_gr <- GRanges(seqnames = loci[,2], ranges = IRanges(start = loci[,3], width = 1))
names(loci_gr) <- loci[,1]

I am not sure why you are trying to modify the code here, I recommend sticking to the example format and modifying your input file so the probe IDs are present.

Cheers,

Tom.

[giorgiabiddau]

Hi Tom,

thank you so much for your answer!

Oh, I created a data frame where the probes IDs were the rownames (and it worked with createGCcontentFile.R), that's why I only have two.
Thanks for the suggestion!

Cheers,

Giorgia