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Preprocessing function to obtain a genomically-ordered list of chromosomes.

Usage

preprocess_object_for_CNV(genes_by_cells = NULL, gene_ann = NULL)

Arguments

genes_by_cells

genes-by-cells input matrix

gene_ann

optional data.frame with gene annotation with mandatory columns "Chromosome", "symbol" and "pos" (genomic location). If NULL gene locations will be collected from org.Hs.eg.db

Value

list of genomically-ordered chromosomes

Details

The preliminary step consist of annotation, duplicates and NA values removal. Then, the matrix is splitted as a list of dataframe, where every dataframe is a chromosome. Chromosomes are ordered from 1 to 22 + X +Y, and then re-ordered by start position.