calculateQC: calculateQC

In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

Description

Calculates the following values for quality control:

Usage

calculateQC(object)

## S4 method for signature 'EMSet'
calculateQC(object)

Arguments

object

An EMSet

Details

qc_libsize:

Total number of counts per cell

qc_ngenes

Number of genes expressed by a cell

qc_ncounts

Total counts per gene

qc_ncells

Number of cells expressing gene

qc_meancounts

Mean expression of the gene

qc_topgeneranking

Rank in most abundant gene expression

qc_pct_total_expression

Proportion of gene expression to total expression

If users have defined controls, the following metrics are also calculated:

qc_nfeaturecounts

Number of reads from non-control genes (feature) for each cell

qc_pctfeatures

Percentage of features to total expression

This function is called when changes are made to the count matrix.

Value

QC values stored in an EMSet's rowData and colData slots

Examples

# Load example dataset
object <- ascend::raw_set

# Recalculate quality control metrics
object <- calculateQC(object)

IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.