quantiseq: Use quanTIseq to deconvolute a gene expression matrix.

In caanene1/Decosus: Method to generate robust consensus from published cell deconvolution/aggregation methods

Use quanTIseq to deconvolute a gene expression matrix.

Description

Function to apply the qunatiseq deconvolution method as described by bioRxiv 223180. https://doi.org/10.1101/223180.

Usage

quantiseq(mix.mat, arrays = FALSE, mRNAscale = TRUE, method = "lsei")

Arguments

mix.mat	The expression matrix to deconvolute, with samples in column and genes in rows.
arrays	The platform used to generate the expression dataset.
mRNAscale	Option to scale expression matrix, defults to TRUE.
method	Option to select the right method, defults to "lsei".

Details

Immune devconvolution using the qunatiseq mnethod described by bioRxiv 223180. https://doi.org/10.1101/223180.

Value

Cell proportions.

t_results

Table of deconvolution across samples.

Note

The user need to ensure that colnames and rownames are set with samples and genes, respectively.

Author(s)

Chinedu A. Anene, PhD

References

https://doi.org/10.1101/223180. https://github.com/FFinotello/quanTIseq

See Also

The output of this function is incorporated directly to the Decosus package for consesus.

caanene1/Decosus documentation built on Feb. 24, 2024, 6:37 a.m.