Error in .normargSEW0(start, "start") : 'start' must be a numeric vector (or NULL)

Question

[bisansamara]

Hi,

I'm using the GenomicRanges package in R to find overlaps between two lists of chromosome ranges. When I use this code, I get an error saying that 'start' must be a numeric vector:

x0 = as.data.frame(read.table("file0.bed")) x1 = read.csv ("file1.csv")

library(GenomicRanges) gr0 = with(x0, GRanges(chr, IRanges(start=start, end=stop)))
Error in .normargSEW0(start, "start") : 'start' must be a numeric vector (or NULL)
gr1 = with(x1, GRanges(chr, IRanges(start=start, end=stop)))

hits = findOverlaps(gr0, gr1) Error in findOverlaps(gr0, gr1) : object 'gr0' not found

I tried to add the command as.numeric to 'start', but i also didn't work:

gr0 = with(x0, GRanges(chr, IRanges(start=as.numeric(start), end=as.numeric(stop))))
Error in as.numeric(start) : cannot coerce type 'closure' to vector of type 'double'

Any suggestions on how to solve this?

Answer 1

[mlweilert]

Your problem lies with the line:

gr1 = with(x1, GRanges(chr, IRanges(start=start, end=stop)))

You are inputting a data.frame object into this command and relying on some assumptions. Check the header information on your data.frame object and make sure the data.frame column names match up to what you entered. This error is a result of incompatible inputs.