runLIAYSON: Main Function.

In liayson: Linking Singe-Cell Transcriptomes Atween Contemporary Subpopulation Genomes

Main Function.

Description

Given an RNA-seq derived cell-by-gene matrix and an DNA-seq derived copy number segmentation, LIAYSON predicts the number of clones present in a tumor, their size, the copy number profile of each clone and the clone membership of each single cell.

Usage

runLIAYSON(X, S, sName, mingps = 20, GRCh = 37, h = 0.2, minSegLength=1E6, outD = NULL)

Arguments

X	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.
S	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.
sName	Sample name.
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.
h	Height at which the tree should be cut (see also cutree).
minSegLength	Minimum number of base pairs below which a segment is to be excluded when defining clones.
outD	The output directory.

Author(s)

Noemi Andor

See Also

clusterCells segmentExpression2CopyNumber

Examples

data(epg)
data(segments)

	out = runLIAYSON(epg, segments, sName="NCI-N87", GRCh = 38, h=0.05)

liayson documentation built on Sept. 30, 2022, 1:07 a.m.