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 2.2.0 Index]