filterCountsData: filterCountsData

In jasonserviss/sp.scRNAseqData: Data and processing functions for the CIMseq.data package

Description

This is a wrapper function for detectLowQualityGenes, detectLowQualityCells.totalCounts, detectLowQualityCells.ERCCfrac, detectLowQualityCells.housekeeping, convertCountsToMatrix. It uses the "cellNumber" column in the metadata to annotate singlets and multiplets and, therefore, the column must be present in the metadata. In addition, singlets should be named "Singlet" in the metadata. The function also checks for the presence of NAs in the counts data and returns an error if NA values are detected.

Arguments

counts	data.frame; The formated counts data.
countsERCC	data.frame; The formated counts ERCC data.
filters	Character; A vector indicating the types of filtering to be performed. Options include: "genes", "totalCounts", "ERCCfrac", and "housekeeping".
geneMinCount	See detectLowQualityGenes
cellMinCount	See detectLowQualityCells.totalCounts
geneName	See detectLowQualityCells.housekeeping
quantileCut	See detectLowQualityCells.housekeeping
percentile	See detectLowQualityCells.ERCCfrac.

Value

A list with the filtered counts as the first element and the filtered ERCC genes as the second element.

Author(s)

Jason Serviss

jasonserviss/sp.scRNAseqData documentation built on Jan. 8, 2020, 11:46 a.m.