I have a BED file that has the following columns: Chromosome number, start, stop, called peaks, and pvalue.

When I run the following code I get an error:

plotManhattan(bedfile = bed, pvalues = bed$pval, col = SushiColors(6), genome = genome, cex = 0.75)

Error:

Error in plot.window(...) : need finite 'ylim' values
In addition: Warning messages:
1: In min(-log10(bedfile[, 5])):
   no non-missing arguments to min; returning Inf
2: In max(-log10(bedfile[, 5])):
   no non-missing arguments to max; returning -Inf

So, this would suggest that there is something wrong with my pvalue column, either NA or something that the log10 function doesn't like.

However, if I manually do: range(-log10(bed$pval)) there are no issues. Additionally, looking at the values themselves, none of them are == 0 and there are no empty cells or NA.

Why isn't this working? I looked at the code for the function and it looks like it attempts to grab the pvalues from the fifth column of whatever you input as your BED file (what is assigned to the bedfile parameter). I'm not sure why it doesn't use what was passed to the pvalue parameter - in fact, this parameter doesn't appear to be used in the function body at all.