mapStatsScopes: mapStats scopes

In CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Description

Functions implementing the scope parameter of the mapStats function.

Usage

msScope_counts(libs)

msScope_mapped(libs)

msScope_qc(libs)

msScope_steps(libs)

msScope_all(libs)

msScope_annotation(libs)

Arguments

libs	A data frame containing metadata describing samples in sequence libraries.

Details

The counts scope reports the number of molecules aligning in promoter, exon, intron and otherwise intergenic. regions.

The mapped scope reports the number of molecules aligning in promoter, exon, intron and otherwise intergenic, plus the number of PCR duplicates (mapped tags minus molecule counts), plus the number of non-properly paired mapped tags.

The qc scope reports the number of tags removed as tag dust, rRNA, spikes, plus the unmapped tags, plus the number of non-properly paired mapped tags, plus the number of PCR duplicates (mapped tags minus molecule counts), plus the number of unique molecule counts.

The steps scope reports the number of tags removed by cleaning, mapping, and deduplication, plus the number of unique molecule counts.

The legacy all scope reports the number of tags in promoters, exons, introns, or mapped elswhere, or removed because they match rRNA or are likely primer artefacts, normalised by the total nubmer of extracted tags.

The legacy annotation scope reports the number of tags in promoters, exons, introns, or mapped elswhere, or removed because they match rRNA or are likely primer artefacts, normalised by the total nubmer of mapped tags.

Value

Returns a list with three elements: libs contains a modified version of the input data frame where columns have been reorganised as needed, colums contains the names of the columns to use for plotting and provides the order of the stacked bars of the plotAnnot function, total indicates the total counts used for normalising the data.

CAGEr documentation built on Jan. 17, 2021, 2 a.m.