genesSummarize: genesSumarize

In mi2-warsaw/sequencingExplainer: Package directRNAExplorer is an R package for dealing with the RNA sequencing data.

Description

Function genesSumarize counts the coverage of each gene

Usage

genesSummarize(bamDataFrame, geneData = directRNAExplorer::TAIR10_genes_tidy,
  chromosome = NULL, range = 0, strand = "sense", genePart = "gene")

Arguments

bamDataFrame	Data frame converted to R using bamToR() function
geneData	Data frame with positions of all genes and their names, by default we use a TAIR10_genes_tidy
chromosome	Optional, number of chromosome
range	How many nucleotide before start and after stop we include to genes.
strand	On which strand we want to compute statistics, by default we use the sense strand, we can also compute statistics on the antisense strand.
genePart	Part of gene on which we compute the summary

Examples

library(directRNAExplorer)
data <- brmDataChromosome1[brmDataChromosome1$pos >2002000 & brmDataChromosome1$pos < 2018000,]
genesSummarize(data)

mi2-warsaw/sequencingExplainer documentation built on May 17, 2019, 4:33 p.m.