% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/calculate_gs_scores.R

\name{calculate_gs_scores}

\alias{calculate_gs_scores}

\title{Calculate gene set scores}

\usage{

calculate_gs_scores(

scMuffinList = NULL,

gs_list = NULL,

mc.cores = 1,

nbins = 25,

nmark_min = 5,

ncells_min = 10,

k = 100,

kmin = 50,

score_type = c("relative", "mean"),

verbose = FALSE,

na.rm = TRUE,

overwrite = FALSE

)

}

\arguments{

\item{scMuffinList}{scMuffinList object}

\item{gs_list}{list of gene sets}

\item{mc.cores}{number of cores}

\item{nbins}{number of bins to split the distribution of average gene expression}

\item{nmark_min}{number of minimum markers that are required for the succesful calculation of a gene set score}

\item{ncells_min}{number of minimum cells in which a gene set has to be succesfully calculated}

\item{k}{number of permutations}

\item{kmin}{minimum number of permutations; due to missing values it is hard to ensure that a gene set score can be compared to k permutations in every cell}

\item{score_type}{type of score. if "relative", than the score is the difference between the observed gene set average expression and that of a k permutations; if "mean" the score is equal to the observed gene set average expression}

\item{verbose}{verbosity}

\item{na.rm}{whether to use NA or not}

\item{overwrite}{whether to update or not gene_set_scoring and gene_set_scoring_full elements of scMuffinList.}

}

\value{

scMuffinList with element gene_set_scoring, a list that contains summary and full. The element summary contains a cells-by-gene sets data.frame. The element "full" contains a data.frame for each gene set. See [gs_score()] for further details.

}

\description{

Calculate gene set scores using the approach described in Tirosh2016

}

\references{

Tirosh2016 10.1126/science.aad0501

}