lapply for GRanges
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@dadbfbf7
Last seen 4 days ago
United States

When I use the 'lapply' function for data in the format of 'GRanges', the system prompts an error, so what are the good solutions? (((Thank you!


data(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
data(Locations)
locs<-Locations
locs.ranges<-GRanges(Locations$chr,IRanges(Locations$pos,Locations$pos))
names(locs.ranges)<-rownames(Locations)
DMR.IDs<-lapply(results.ranges,function(x) names(locs.ranges[locs.ranges %over% x]))

GRanges objects don't support [[, as.list(), lapply(), or unlist() at the
  moment 

sessionInfo( )
lapply GRanges • 154 views
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Entering edit mode
@herve-pages-1542
Last seen 4 hours ago
Seattle, WA, United States

You can loop on a GRanges object, if you really want to, by doing something like this:

DMR.IDs <- lapply(seq_along(results.ranges), function(i) names(locs.ranges[locs.ranges %over% results.ranges[i]]))

However, keep in mind that lapply-based solutions tend to be quite inefficient so should be avoided whenever possible. In your case a much better way is to do:

hits <- findOverlaps(results.ranges, locs.ranges)
DMR.IDs <- extractList(names(locs.ranges), as(hits, "IntegerList"))

This will be thousands times more efficient ;-)

Cheers,

H.

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