Empty 3'UTR APA RE table from PASEXP_3UTR function

[faricazjj]

Hi Ruijia,

I am running PASEXP_3UTR to get the relative expression of APA sites in 3UTR with this bam file and this gtf file

The code I used to generate the above outputs is below:

#----------------------Build the PAS reference regions----------------------
PASREFraw = PAS2GEF(GTFfile, AnnoMethod="V2")
refUTRraw = PASREFraw$refUTRraw
dfIPAraw = PASREFraw$dfIPA
dfLEraw = PASREFraw$dfLE
PASREF = REF4PAS(refUTRraw,dfIPAraw,dfLEraw)
# reference region used for 3'UTR APA analysis
UTRdbraw = PASREF$UTRdbraw
# dfIPA and dfLE are needed in intronic APA analysis
dfIPA = PASREF$dfIPA
dfLE = PASREF$dfLE

#----------Calculation of relative expression of 3'UTR APA and IPA----------
# calculate relative expression of 3' UTR APA
UTR_APA_OUT = PASEXP_3UTR(UTRdbraw, flsall, Strandtype = "NONE")

# ensure that coordinates are numeric
dfIPA$Pos = as.numeric(as.character(dfIPA$Pos))
dfIPA$upstreamSS = as.numeric(as.character(dfIPA$upstreamSS))
dfIPA$downstreamSS = as.numeric(as.character(dfIPA$downstreamSS))
dfLE$LEstart = as.numeric(as.character(dfLE$LEstart))
dfLE$TES = as.numeric(as.character(dfLE$TES))

# calculate relative expression of IPA
IPA_OUT = PASEXP_IPA(dfIPA, dfLE, flsall, Strandtype = opt$strandtype, nts = 1)
print("Relative expression of 3'UTR APA")
print(UTR_APA_OUT)
print("Relative expression of IPA")
print(IPA_OUT)

where flsall is a data frame with the path to the input bam file

                           srsf3_replicate1_1
"../../tests/test_data/siSrsf3_R1_2genes.bam"