filter_RNA_seq {GWENA} | R Documentation |
Keeping genes with at least one sample with count above min_count in RNA-seq data.
filter_RNA_seq( data_expr, min_count = 5, method = c("at least one", "mean", "all") )
data_expr |
matrix or data.frame or SummarizedExperiment, table of expression values (either microarray or RNA-seq), with genes as column and samples as row. |
min_count |
integer, minimal number of count to be considered in method. |
method |
string, name of the method for filtering. Must be one of "at least one", "mean", or " all" |
Low counts in RNA-seq can bring noise to gene co-expression module building, so filtering them help to improve quality.
A data.frame of filtered genes
df <- matrix(abs(rnorm(15*45)), 15) * 3 colnames(df) <- paste0("gene_", seq_len(ncol(df))) rownames(df) <- paste0("sample_", seq_len(nrow(df))) df_filtered <- filter_RNA_seq(df)