rliger: getGeneValues – R documentation

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getGeneValues

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

## Not run: 
# liger object with factorization complete
# ligerex
gene_values <- getGeneValues(ligerex@raw.data, 'MALAT1')

## End(Not run)

rliger

Linked Inference of Genomic Experimental Relationships

v1.0.0

GPL-3

Authors

Joshua Welch [aut, ctb], Chao Gao [aut, ctb, cre], Jialin Liu [aut, ctb], Joshua Sodicoff [aut, ctb], Velina Kozareva [aut, ctb], Evan Macosko [aut, ctb], Paul Hoffman [ctb], Ilya Korsunsky [ctb], Robert Lee [ctb]

Initial release

2021-04-18