filter_prop_zero: Filter Genes for by Max Proportion Zero Among Groups

In LieberInstitute/TREG: Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Filter Genes for by Max Proportion Zero Among Groups

Description

This function uses the data.frame() generated to find the maximum Proportion Zero across groups, then filter to a set of genes that pass the max Prop Zero cutoff defined by the user.

Usage

filter_prop_zero(prop_zero_df, cutoff = 0.9, na.rm = TRUE)

Arguments

prop_zero_df	data.frame() containing proportion of zero counts, genes as rows, groups as columns.
cutoff	A numeric() cutoff value for maximum Proportion Zero. The cutoff value should be < 1.
na.rm	a logical indicating whether missing values should be removed when max prop_zero is calculated.

Value

A character() of gene names that are under the cutoff. These names are from the rownames() of the expression data.

See Also

Other Proportion Zero functions: get_prop_zero()

Examples

## Get Proportion Zero data.frame
prop_zero <- get_prop_zero(sce_zero_test, group_col = "group")

## Filter with max Proportion Zero cutoff = 0.59
filter_prop_zero(prop_zero, cutoff = 0.59)

## NA handling
prop_zero[1, 1] <- NA

## If NA are present in the prop_zero_df the user can choose to:

## Remove NAs (default)
## genes with NA counts may be included in the final list
filter_prop_zero(prop_zero, cutoff = 0.59, na.rm = TRUE)

## Include NA values
## any gene with genes with NA counts (so max prop_zero will be NA)
## will be removed from the final list, this will throw warning
filter_prop_zero(prop_zero, cutoff = 0.59, na.rm = FALSE)

LieberInstitute/TREG documentation built on Dec. 15, 2024, 12:24 p.m.