liayson (version 1.0.5)

aggregateSegmentExpression: Aggregating genes across copy number segments.

Description

Calculates average expression of genes grouped by common segment membership.

Usage

aggregateSegmentExpression(epg, segments, dataset="hsapiens_gene_ensembl", 
						mingps = 20, GRCh = 37, host=NULL)

Value

List with fields:

eps

Segment-by-cell matrix of expression values.

gps

Segment-by-cell matrix of the number of expressed genes.

Arguments

epg

Gene-by-cell matrix of expression. Recommendation is to cap extreme UMI counts (e.g. at the 99% quantile) and to include only cells expressing at least 1,000 genes.

segments

Matrix in which each row corresponds to a copy number segment as calculated by a circular binary segmentation algorithm. Has to contain at least the following column names:
chr - chromosome;
startpos - the first genomic position of a copy number segment;
endpos - the last genomic position of a copy number segment;
CN_Estimate - the copy number estimated for each segment.

dataset

Dataset to download from BioMart.

mingps

Minimum number of expressed genes a segment needs to contain in order to be included in output.

GRCh

Human reference genome version to be used for annotating gene coordinates.

host

Host address used by BioMart.

Author

Noemi Andor

Details

Let S := { \(S_1, S_2, ... S_n\) } be the set of \(n\) genomic segments that have been obtained from DNA-sequencing a given sample (e.g. from bulk exome-sequencing, scDNA-sequencing, etc.). Genes are mapped to their genomic coordinates using the biomaRt package and assigned to a segment based on their coordinates. Genes are grouped by their segment membership, to obtain the average number of UMIs and the number of expressed genes per segment \(S_j\) per cell i.

Examples

data(epg)
data(segments)
# \donttest{
	X=aggregateSegmentExpression(epg, segments, mingps=20, GRCh=38)
# }