liayson (version 1.0.5)

runLIAYSON: 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

Noemi Andor

See Also

clusterCells segmentExpression2CopyNumber

Examples

data(epg)
data(segments)
# \donttest{
	out = runLIAYSON(epg, segments, sName="NCI-N87", GRCh = 38, h=0.05)
# }