getGeneValues: Get gene expression values from list of expression matrices.

In rliger: Linked Inference of Genomic Experimental Relationships

Get gene expression values from list of expression matrices.

Description

Returns single vector of gene values across all datasets in list provided. Data can be in raw, normalized or scaled form. If matrices are in cell x gene format, set use.cols = TRUE.

Usage

getGeneValues(
  list,
  gene,
  use.cols = FALSE,
  methylation.indices = NULL,
  log2scale = FALSE,
  scale.factor = 10000
)

Arguments

list	List of gene x cell (or cell x gene) matrices
gene	Gene for which to return values (if gene is not found in appropriate dimnames will return vector of NA).
use.cols	Whether to query columns for desired gene (set to TRUE if matrices are cell x gene) (default FALSE).
methylation.indices	Indices of datasets with methylation data (never log2scaled) (default NULL).
log2scale	Whether to log2+1 scale (with multiplicative factor) values (default FALSE).
scale.factor	Scale factor to use with log2 scaling (default 10000).

Value

Plots to console (1-2 pages per factor)

Examples

NKG7 <- getGeneValues(list(ctrl = ctrl, stim = stim), "NKG7")

rliger documentation built on Nov. 9, 2023, 1:07 a.m.