Fish error; there are no seqlevels of events that match hypothesis #7
Description
library(fishHook)
library(gTrack)
library(rtracklayer)
mutations = dt2gr(fread('test_150_maftools.maf'))
genes = gr.sub(import('gencode.v27.annotation.gtf'))
genes = genes %Q% (gene_type == 'protein_coding') %Q% (level<3)
cds = import("gencode.v27.annotation.gtf")
exomecov = import('Z_NSLA_1004_T.bw')
head(mutations[, c('Tumor_Sample_Barcode', 'Variant_Type', 'Variant_Classification', 'Reference_Allele', 'Tumor_Seq_Allele2')])
eligible = exomecov %Q% which(score>0.95)
eligible = reduce(intersect(eligible, cds, ignore.strand = TRUE))
events = mutations %Q% (Variant_Classification != 'Silent')
fish = Fish(hypotheses = genes[, 'gene_name'], events = events, eligible = eligible, idcol = 'Tumor_Sample_Barcode')
Error in .subset2(public_bind_env, "initialize")(...) :
Error: there are no seqlevels of events that match hypotheses
In addition: Warning messages:
1: In .subset2(public_bind_env, "initialize")(...) :
Warning: seqlevels of Hypotheses and Eligible appear to be in different formats
2: In .subset2(public_bind_env, "initialize")(...) :
Warning: seqlevels of Hypotheses and Events appear to be in different formats
