get_totalCov: Calculate the total coverage

View source: R/08.get_totalCov.R

get_totalCovR Documentation

Calculate the total coverage

Description

For hugeData, coverage of samples in each condition is merged chromosome by chromosome. For non-hugeData, per-chromosome coverage of all samples

Usage

get_totalCov(sqlite_db, chr.cov, seqname, metadata, outdir, hugeData)

Arguments

sqlite_db

A path to the SQLite database for InPAS, i.e. the output of setup_sqlitedb().

chr.cov

A list of Rle objects storing coverage per sample for a given chromosome/scaffold

seqname

A character(1), the chromosome/scaffold name

metadata

A data frame containing the metadata for a RNA-seq experiment, which can be extract from the SQLite database set up by setup_sqlitedb()

outdir

A character(1) vector, a path with write permission for storing InPAS analysis results. If it doesn't exist, it will be created.

hugeData

A logical(1), indicating whether it is huge data

Value

A list containing pooled coverage data. For hugeData, coverage of samples under each condition is merged chromosome by chromosome. For non-hugeData, per-chromosome coverage of all samples are returned.

seqname

chromosome/scaffold name

condition1

condition name 1

condition1

condition name 2

Author(s)

Haibo Liu, Jianhong Ou


haibol2016/InPAS documentation built on March 30, 2022, 10:30 a.m.