get_totalCov {InPAS}R 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 are returned.

Usage

get_totalCov(sqlite_db, seqname, hugeData)

Arguments

sqlite_db

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

seqname

A character(1), the chromosome/scaffold name

hugeData

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

Value

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

seqname

chromosome/scaffold name

tag1

name tag for sample1

tag2

name tag for sample2

tagN

name tag for sampleN

Author(s)

Haibo Liu, Jianhong Ou


[Package InPAS version 2.1.0 Index]