normalized: normalize gene expressions for sra metadata database

In SiruoWang/srametadata: Getting and cleaning metadata from Sequence Read Archive (SRA)

Description

normalize gene expressions for sra metadata database

Usage

normalized(file, path, chr, start, end)

Arguments

file	file:filename
path	path used in the .sh file
chr	chr specify which chromosome is inspected
start	start specify the starting position of the inspected gene
end	end specify the ending position of the inspected gene

Value

a normalized gene expression dataframe

Examples

library(rtracklayer)
library(GenomicRanges)
normalized(file = scan("sra_samples.txt", what="", sep="\n"), path = path, chr = "chrY", start = 14813160, end = 14972768)

SiruoWang/srametadata documentation built on May 9, 2019, 1:47 p.m.