get_totalCov: Calculate the total coverage

In haibol2016/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

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.