You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
bed <- "overlap_flag_coordinates_with_r_duplicates_removed.bed"
bed_df <- read.table(bed, header = FALSE, sep="\t",stringsAsFactors=FALSE, quote="")
#1:
toGRanges(bed, format="BED")
# Error: each range must have an end that is greater or equal to its start minus one
#2:
toGRanges(bed_df)
# Error: Error in (function (data, colNames = NULL, format = "", ...) :
colname must contain space/seqnames, start and end.
# I manually checked, the (ends - starts) are strictly larger than 1.
#3:
toGRanges(bed, format="narrowPeak")
# this works
ChIPpeakAnno_3.26.4
The above suggests that toGRanges() might have some glitch with dealing with "BED" format.
The text was updated successfully, but these errors were encountered:
Hi Jianhong,
This is related to the issue posted at https://support.bioconductor.org/p/9141976/#9142000.
I tested with the following commands:
The text was updated successfully, but these errors were encountered: