| StandardChromNameNew | R Documentation |
Standardize the chromosome name annotations for a data frame.
StandardChromNameNew(df, name.of.VCF = NULL)
df |
An in-memory data.frame representing a VCF. |
name.of.VCF |
Name of the VCF file. |
A list with the elements
df a data frame with variants that had "legal" chromosome
names (see below for illegal chromosome names).
Leading "chr" strings are removed.
discarded.variants: Non-NULL only if there
variants with illegal chromosome names; these are
names that contain the strings "GL", "Hs", "KI", "M", "random".