aggregateSegmentExpression: Aggregating genes across copy number segments.

Description Usage Arguments Details Value Examples

View source: R/aggregateSegmentExpression.R

Description

Calculates average expression of genes grouped by common segment membership.

Usage

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Arguments

epg

Gene-by-cell matrix of expression. Recommendation is to cap UMI counts at the 99

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. Recommendation is to exclude genomic segments in which the average number of expressed genes per cell is below 20.

mingps

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

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.

Value

List with fields:

eps

Segment-by-cell matrix of expression values.

gps

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

Examples

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data(epg)
data(segments)
X=aggregateSegmentExpression(epg, segments, mingps=20, GRCh=38)

##View output: 
library(futile.matrix)
lapply(X, peek)

noemiandor/liayson documentation built on Oct. 27, 2018, 12:15 a.m.