getGeneValues {rliger} | R Documentation |
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")
[Package rliger version 1.0.1 Index]