findHVG-DM: Find HVG with the DM approach

In BPijuanSala/proSeq: Tools to preprocess RNA-seq data

Description

It finds highly variable genes using the distance-to-median method proposed in Kolodziejczyk et al. Cell Stem Cell, 2015. I adapted the code from Ximena Ibarra-Soria.

Usage

findHVG.DM(data, qMinThr = 0.9, qThr = 0.8, plot = FALSE)

Arguments

data	Please provide the data without any transformation (e.g. log10).
qMinThr	Quantile threshold to discard lowly expressed genes.E.g. if set to 0.9, it will take the data with median above the quantile 0.9 and compute the DM. The ones below (bottom 90%) will be discarded. Default: 0.9.
qThr	Quantile threshold from which to consider a gene highly variable. E.g. If set to 0.8, it will take the most HVG genes falling on the top 20%. Default: 0.8
plot	Logical. Default: FALSE.

Value

vector of HVG.

Author(s)

Blanca Pijuan-Sala.

References

Kolodziejczyk et al. Cell Stem Cell, 2015.

BPijuanSala/proSeq documentation built on May 30, 2019, 11:47 p.m.