generateCorrectedIsoform: generateCorrectedIsoform generates the corrected isoforms...

In zhushijia/STAR2bSMRT: STARlong and STARshort based Single Molecule Real Time Iso-Seq analysis

Description

generateCorrectedIsoform generates the corrected isoforms given the defined thresholds of ts and td

Usage

generateCorrectedIsoform(LRjunc, SRjunc, LRtag, LRread, ts, td,
  matchedLS = NULL, fuzzyMatch = 100)

Arguments

LRjunc	a list of data frame, indicating the splicing junction sites obtained from long reads
SRjunc	a list of data frame, indicating the splicing junction sites obtained from short reads
LRtag	a list of character values, indicating the splicing junctions for each long read in the format of "junction_start,junction_end"
LRread	a list of data frame, indicating the information of long read, comprising id, chr, strand, start, end, junc
ts	integer value indicating the number of short read support
td	integer value indicating the distance between long and short read junction sites
matchedLS	the correspondence bewteen long read and short read-derived junction sites
fuzzyMatch	integer value indicating the tolerance distance

Value

a list of corrected isoforms, comprising the following items:

• isoform a list of isoforms: data frame of junction sites

• uniNum integer value indicating the number of unique isoforms

• frac numeric value indicating the fraction of corrected reads relative to total read counts

• isoformCount integer value indicating the read count for each isoform

• LSjuncCount data frame representing the information of each isoform, comprising columns: srCount, chr, start, end, motif, and lrCount

• normalizedIsoformCount numeric values indicating the normalized read count for each isoform when integrating multiple smrtcells

zhushijia/STAR2bSMRT documentation built on Dec. 18, 2019, 7:37 a.m.