SwarnTopTags: This function selects the top genes in scRNA-seq data.

In sam-uofl/SwarnSeq: Detection of Differentially Expressed Genes from Single Cell RNA-seq Data

Description

This function selects the top genes in scRNA-seq data.

Usage

SwarnTopTags(results, m)

Arguments

results	A output data frame from SwarnSeqLRT or SwarnUnadjLRT which contains the unclassified differential expression analysis results.
m	A scalar representing the number of top performing genes to be selected from the scRNA-seq data.

Value

A list of the top genes along with their statistics.

Author(s)

Samarendra Das

See Also

SwarnSeqLRT, for the detection of differentially expressed genes from scRNA-seq data.

TestData, a test dataset for SwarnSeq.

Examples

 #Load the test count data, spike-in counts and spike-in concentration data for SwarnSeq.
data(TestData)
counts <- TestData$CountData
Spikes <- TestData$SpikeCounts
SpikeConc <- TestData$SpikeConc

#specifying the group information, the group 1 and 2 have two hundred cells each.
group <- c(rep(1, 200), rep(2, 200))
#Specifying the cluster memberships of the cells in columns of countData.
cellcluster <- c(rep(1, 60), rep(2, 40), rep(3, 50),
                    rep(4, 50), rep(5, 30),
                    rep(6, 90),
                    rep(7, 80))

#results <- SwarnSeqLRT(CountData=counts, RNAspike.use=TRUE, spikes=Spikes, spike.conc=SpikeConc,
                      #parallel=FALSE, norm.method="TMM", group=group, CellCluster=cellcluster,
                          #CellAuxil=NULL, maxit=500, eps=1e-10,
                          #muoffset=NULL, phioffset=NULL, weights=NULL, p.adjust.method="hochberg")

#DEGtypes <- SwarnTopTags(results, m = 100)

sam-uofl/SwarnSeq documentation built on Sept. 6, 2020, 12:09 a.m.