getGAlignmentsPairs {ORFik}R Documentation

Internal GAlignmentPairs loader from fst data.frame

Description

Internal GAlignmentPairs loader from fst data.frame

Usage

getGAlignmentsPairs(df, strandMode = 0)

Arguments

df

a data.frame with columns minimum 6 columns: seqnames, start1/start2 (integers), cigar1/cigar2 and strand
Additional columns will be assigned as meta columns

strandMode

numeric, default 0. Only used for paired end bam files. One of (0: strand = *, 1: first read of pair is +, 2: first read of pair is -). See ?strandMode. Note: Sets default to 0 instead of 1, as readGAlignmentPairs uses 1. This is to guarantee hits, but will also make mismatches of overlapping transcripts in opposite directions.

Value

GAlignmentPairs object


[Package ORFik version 1.10.13 Index]