gene_exp: Differential Gene Expression plots

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

Description

write a desc

Usage

gene_exp(sysma, mytargets, type = "SYSargs", x, y, con)

Arguments

sysma	path to 'param' file; file structure follows a simple name/value syntax that converted into JSON format; for details about the file structure see sample files provided by package. Assign NULL to run the pipeline without 'param' file. This can be useful for running partial workflows, e.g. with pregenerated BAM files.
mytargets	path to targets file
type	type="SYSargs" returns SYSargs, type="json" returns param file content in JSON format (requires rjson library)
x	used for ploting the data to specify weather the data is paired-end or single end
y	used for plotting the data to indicate the count of data
con	a formula which expresses how the counts for each gene depend on the variables in colData

See Also

edgeR

Examples

## Not run: 
pairs <- c( "paired-end", "paired-end", "paired-end","paired-end","paired-end","paired-end")
count <- c(1,1,2,2,3,3)
condition <- factor(c("N1","N1","N2","N2","M1","M1","M2","M2","M3","M3","M4","M4","U1","U1"))
gene_exp(sysma="./param/tophat.param", mytargets="targetsPE.txt", x = pairs, y = count, con = condition)

## End(Not run)

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