splice: alternative splicing analysis

In DISC-IISR/RNAseqAnalysis: A List of Relevent Functions RNA-seq data analysis

Description

Its an Integrative function for the analysis of alternative splicing. it provides with Alternative splicing discovery using junctions and DE and DU estimation.

Usage

splice(pairs, group, colour, bamFiles)

Arguments

pairs	Vector of length two, either numeric or character, providing the pair of groups to be compared
group	Factorial vector with tags for each sample
colour	Vector containing color for each condition
bamFiles	The path to bam files

See Also

ASpli

Examples

## Not run: 
bamfiles <- c("extdata/A83.bam", "extdata/A84.bam", "extdata/A85.bam", "extdata/A86.bam", "extdata/A94.bam", "extdata/A95.bam")
bamfiles <- c("extdata/SRR5253683.bam", "extdata/SRR5253684.bam", "extdata/SRR5253685.bam",
 "extdata/SRR5253686.bam", "extdata/SRR5253687.bam", "extdata/SRR5253688.bam","extdata/SRR5253689.bam",
 "extdata/SRR5253690.bam","extdata/SRR5253691.bam","extdata/SRR5253692.bam","extdata/SRR5253694.bam",
"extdata/SRR5253695.bam","extdata/SRR5253696.bam","extdata/SRR5253697.bam")
col <- c("red","yellow","green")
col <- c("red","yellow","green","blue", "black", "pink", "violet")
grp <- c(rep("U1", 2),rep("M3", 2),rep("N1", 2))
grp <- c(rep("N1", 2),rep("N2", 2),rep("M1", 2),rep("M2", 2),rep("M3", 2),rep("M4", 2),rep("U1", 2))
splice(pairs = c("U1", "M3"), group = grp, colour = col, bamFiles=bamfiles)

## End(Not run)


## Not run: 
bamfiles <- c("extdata/A83.bam", "extdata/A84.bam", "extdata/A85.bam", "extdata/A86.bam", "extdata/A94.bam", "extdata/A95.bam")
bamfiles <- c("extdata/SRR5253683.bam", "extdata/SRR5253684.bam", "extdata/SRR5253685.bam",
 "extdata/SRR5253686.bam", "extdata/SRR5253687.bam", "extdata/SRR5253688.bam","extdata/SRR5253689.bam",
 "extdata/SRR5253690.bam","extdata/SRR5253691.bam","extdata/SRR5253692.bam","extdata/SRR5253694.bam",
"extdata/SRR5253695.bam","extdata/SRR5253696.bam","extdata/SRR5253697.bam")
col <- c("red","yellow","green")
col <- c("red","yellow","green","blue", "black", "pink", "violet")
grp <- c(rep("U1", 2),rep("M3", 2),rep("N1", 2))
grp <- c(rep("N1", 2),rep("N2", 2),rep("M1", 2),rep("M2", 2),rep("M3", 2),rep("M4", 2),rep("U1", 2))
splice(pairs = c("U1", "M3"), group = grp, colour = col, bamFiles=bamfiles)

## End(Not run)

DISC-IISR/RNAseqAnalysis documentation built on May 9, 2019, 8:10 a.m.