getAllSPVs: Get surrogate proportion variables (SPVs)

In mchikina/CellCODE: Cell type COmputational Differential Estimation.

Description

Estimates SPVs from data and cell type markers.

Usage

getAllSPVs(data, grp, dataTag, method = c("mixed", "raw", "residual", "SVA"), plot = F, mix.par = 0.3)

Arguments

data	A matrix of expression data.
grp	A factor of group assignments. Same size as ncol(data).
dataTag	A matrix of cell type markers as those produced by the tagData function. Genes are in rows and cell types are in columns. A non-zero value in row i column j indicates that a gene i is a marker for cell type j.
method	The method used to account for the group effect when estimating SPVs. mixed: The suggested method. Attempts to figure out which genes are differentially expressed at the single cell level and remove those from SPV estimation. raw: Does not account for group effect. Uses all genes as is. residual: Group effect is removed before SPV estimations. SPVs will have equal within group means. SVA: Same idea as mixed but uses the default SVA framework.
plot	Whether or not the results should be plotted as a correlation heatmap.
mix.par	The fraction of genes to remove in the mixed method. The default parameter is usually suitable.

Value

A sample by cell-type matrix of surrogate proportion variables.

mchikina/CellCODE documentation built on May 23, 2019, 1:13 p.m.