getGAlignmentsPairs: Internal GAlignmentPairs loader from fst data.frame

In ORFik: Open Reading Frames in Genomics

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

ORFik documentation built on March 27, 2021, 6 p.m.