get.top.signature.dat: Obtain the top signature genes and related information

In ProFAST: Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

Obtain the top signature genes and related information

Description

Obtain the top signature genes and related information.

Usage

get.top.signature.dat(df.list, ntop = 5, expr.prop.cutoff = 0.1)

Arguments

df.list	a list that is obtained by the function find.signature.genes.
ntop	an optional positive integer, specify the how many top signature genes extracted, default as 5.
expr.prop.cutoff	an optional postive real ranging from 0 to 1, specify cutoff of expression proportion of features, default as 0.1.

Details

Using this funciton, we obtain the top signature genes and organize them into a data.frame. The 'row.names' are gene names. The colname 'distance' means the distance between gene (i.e., VPREB3) and cells with the specific cell type (i.e., B cell), which is calculated based on the coembedding of genes and cells in the coembedding space. The distance is smaller, the association between gene and the cell type is stronger. The colname 'expr.prop' represents the expression proportion of the gene (i.e., VPREB3) within the cell type (i.e., B cell). The colname 'label' means the cell types and colname 'gene' denotes the gene name. By the data.frame object, we know 'VPREB3' is the one of the top signature gene of B cell.

Value

return a 'data.frame' object with four columns: 'distance','expr.prop', 'label' and 'gene'.

References

None

See Also

None

Examples

library(Seurat)
data(pbmc3k_subset)
pbmc3k_subset <- pdistance(pbmc3k_subset, reduction='ncfm')
df_list_rna <- find.signature.genes(pbmc3k_subset)
dat.sig <- get.top.signature.dat(df_list_rna, ntop=5)
head(dat.sig)

ProFAST documentation built on May 29, 2024, 7:15 a.m.