mra {corto}R Documentation

Perform Master Regulator Analysis (mra).

Description

The analysis is performed between two groups of samples in the form of expression matrices, with genes/features as rows and samples as columns.

Usage

mra(
  expmat1,
  expmat2 = NULL,
  regulon,
  minsize = 10,
  nperm = NULL,
  nthreads = 2,
  verbose = FALSE,
  atacseq = NULL
)

Arguments

expmat1

A numeric expression matrix, with genes/features as rows and samples as columns. If only expmat1 is provided (without expmat2), the function will perform a sample-by-sample master regulator analysis, with the mean of the dataset as a reference. If expmat2 is provided, expmat1 will be considered the "treatment" sample set. If a named vector is provided, with names as genes/features and values as signature values (e.g. T-test statistics), signature master regulator analysis is performed.

expmat2

A numeric expression matrix, with genes/features as rows and samples as columns. If provided, it will be considered as the "control" or "reference" sample set for expmat1.

regulon

A _regulon_ object, output of the _corto_ function.

minsize

A minimum network size for each centroid/TF to be analyzed. Default is 10.

nperm

The number of times the input data will be permuted to generate null signatures. Default is 1000 if expmat2 is provided, and 10 if expmat2 is not provided (single sample mra).

nthreads

The number of threads to use for generating null signatures. Default is 1

verbose

Boolean, whether to print full messages on progress analysis. Default is FALSE

atacseq

An optional 3 column matrix derived from an ATAC-Seq analysis, indicating 1) gene symbol, 2) -log10(FDR)*sing(log2FC) of an ATAC-Seq design, 3) distance from TSS. If provided, the output will contain an _atacseq_ field.

Value

A list summarizing the master regulator analysis


[Package corto version 1.1.6 Index]