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.