al2na
commented
2 years ago it seems there are some contigs in one object that are not present in the other one and this causes problems with the overlap operation. if you can make the some objects pair work in functions like GenomicRanges::findOverlaps or equivalent genomation functions should also work
On Fri, Nov 19, 2021 at 8:22 AM frylhc @.***> wrote:
Hi everyone, I am trying to plot a pie chart using annotateWithFeatures, the pie chart indicate the proportion of all methylated sites in each genomic features (CDS,5'UTR,3'UTR,intron,promoter,intergenic). First, I used GenomicRanges package to construct the GRangesList required by annotateWithFeatures. Then, I used annotateWithFeatures to obtain the results, but an error occured. Could you please help me with this? Thanks.
`Error in no.of.OlapFeat[match(hits$annot, names(features))] <- hits$featureHits : NAs are not allowed in subscripted assignments In addition: Warning message: In .Seqinfo.mergexy(x, y) : Each of the 2 combined objects has sequence levels not in the other:
- in 'x': UAContig42, UAContig43
- in 'y': UAContig12, UAContig18, UAContig19, UAContig20, UAContig21, UAContig25, UAContig26, UAContig29, UAContig40, UAContig45 Make sure to always combine/compare objects based on the same reference genome (use suppressWarnings() to suppress this warning). `
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frylhc
Hi everyone, I am trying to plot a pie chart using annotateWithFeatures, the pie chart indicate the proportion of all methylated sites in each genomic features (CDS,5'UTR,3'UTR,intron,promoter,intergenic). First, I used GenomicRanges package to construct the GRangesList required by annotateWithFeatures. Then, I used annotateWithFeatures to obtain the results, but an error occured. Could you please help me with this? Thanks.
`Error in no.of.OlapFeat[match(hits$annot, names(features))] <- hits$featureHits : NAs are not allowed in subscripted assignments In addition: Warning message: In .Seqinfo.mergexy(x, y) : Each of the 2 combined objects has sequence levels not in the other: