View source: R/aggregateSegmentExpression.R
aggregateSegmentExpression | R Documentation |
Calculates average expression of genes grouped by common segment membership.
aggregateSegmentExpression(epg, segments, mingps = 20, GRCh=37)
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: |
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. |
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.
List with fields:
eps |
Segment-by-cell matrix of expression values. |
gps |
Segment-by-cell matrix of the number of expressed genes. |
Noemi Andor
data(epg) data(segments) X=aggregateSegmentExpression(epg, segments, mingps=20, GRCh=38)
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