new version has bug with all locusdef except for nearest_TSS

[nlthanhthanh]

Hello,

I tried to run chipenrich both in r and on the website, and it seems that only locusdef="nearest_TSS" works

results <- chipenrich(peaks = chip_seq, genome = 'hg19', genesets = gs_path,locusdef = "nearest_tss", qc_plots = TRUE, out_name = NULL, n_cores = 1)

When I changed locusdef to "nearest_gene", "5kb", "10kb", I received this error:
Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length

Appreciate if you have suggestions! Thanks

[wangk4]

Hello,

I tried to run chipenrich both in r and on the website, and it seems that only locusdef="nearest_TSS" works

results <- chipenrich(peaks = chip_seq, genome = 'hg19', genesets = gs_path,locusdef = "nearest_tss", qc_plots = TRUE, out_name = NULL, n_cores = 1)

When I changed locusdef to "nearest_gene", "5kb", "10kb", I received this error: Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length

Appreciate if you have suggestions! Thanks

Hi, I did a test run and cannot repeat this error message. Could you please give me more detail about your input data and your R code?
The input data should only contain three columns (see the following example), the column names could be "seqname", "start", "end".
chr20 26189744 26190104
chr6 119558422 119558782
chr16 14580748 14581108
chr2 133016741 133017101
chr14 88237590 88237950
chr9 131843162 131843522

Also, you can use supported_genesets() function to check which gene set are currently available for running chipenrich function.