baseScores: Basic Scoring of Matrix by Gene sigs

In jlaffy/scalop: Single Cell Analysis Operations

Basic Scoring of Matrix by Gene sigs

Description

Average expression level of each column in m for (each) sig(s) in <sigs>.

Usage

baseScores(m, sigs, conserved.genes = 0.7)

Arguments

m	a non-centered matrix of genes X cells/samples. The matrix will be row-centered internally prior to scoring.
sigs	a character vector of genes or list of character vectors. Sigs will be filtered to remove genes that are missing from rows in <m>.
conserved.genes	minimum fraction of genes retained in sigs after filtering that is allowed. sigs not passing this cutoff will not be used to score the matrix. This can be ignored if all genes in sigs are present in rownames(<m>). Default: 0.7

Value

a dataframe of scores, with as many rows as there are columns in <m> and as many columns as there are <sigs> to score against.

jlaffy/scalop documentation built on March 24, 2024, 9 a.m.