filter_genes_without_1to1_homolog {EWCE}

R Documentation

filter_genes_without_1to1_homolog

Description

filter_genes_without_1to1_homolog Takes the filenames of celltype_data files, loads them, and drops any genes which don't have a 1:1 homolog based on biomart. The new files are saved to disc, appending '_1to1only' to the file tag of the previous file.

Usage

filter_genes_without_1to1_homolog(filenames)

Arguments

filenames

Array of filenames for sct_data saved as .Rda files

Value

Array of filenames included the ones with only 1:1 homologs

Examples

library(ewceData)
# Load the single cell data
cortex_mrna <- cortex_mrna()
expData <- cortex_mrna$exp
expData <- expData[1:100, ] # Use only a subset to keep the example quick
l1 <- cortex_mrna$annot$level1class
l2 <- cortex_mrna$annot$level2class
annotLevels <- list(level1class = l1, level2class = l2)
fNames_ALLCELLS <- generate_celltype_data(exp = expData,
    annotLevels = annotLevels,
    groupName = "allKImouse")
fNames_ALLCELLS <- filter_genes_without_1to1_homolog(fNames_ALLCELLS)

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