SEcalculation: Splicing Efficiency Calculation

In SEAA: Splicing Efficiency Analysis and Annotation

Description

This function is used to calculate the splicing efficiency.

Usage

SEcalculation(BAM_files, Anno_SAF, paired = TRUE, thread = 1, strand = 1)

Arguments

BAM_files	Aligned reads stored in indexed bam files.(2 bam files)
Anno_SAF	Splicing sites annotation in a saf file.
paired	Whether the sequencing is paired or not.
thread	threads number used in calculating
strand	which strand of the sequencing

Value

a large list

Examples

BAM_files <- c("~/project3tB/SEAA_project/R_counstruction_place/SEAA/inst/extdata/NC_t.bam",
"~/project3tB/SEAA_project/R_counstruction_place/SEAA/inst/extdata/USP_t.bam")
Anno_SAF<-"~/project3tB/SEAA_project/R_counstruction_place/SEAA/inst/extdata/test.saf"
SEresultlist<-SEcalculation(BAM_files,Anno_SAF,paired = TRUE ,thread = 2,strand = 1)

SEAA documentation built on Sept. 19, 2021, 9:07 a.m.