methylcheck.exclude_sex_control_probes

methylcheck.exclude_sex_control_probes(df, array, no_sex=True, no_control=True, verbose=False)

Exclude probes from an array, and return a filtered array.

df: dataframe of beta values or m-values. array: type of array used.

{‘27k’, ‘450k’, ‘EPIC’, ‘EPICPLUS’, ‘MOUSE’} or {‘IlluminaHumanMethylation27k’,’IlluminaHumanMethylation450k’,’IlluminaHumanMethylationEPIC’, ‘mouse’} or {‘27k’, ‘450k’, ‘epic’, ‘epic+’, ‘mouse’}

no_sex: bool

(default True) if True, will remove all probes that target X and Y chromosome locations, as they are sex specific – and lead to multiple clusters when trying to detect and remove outliers (noisy data).

no_control: bool

(default True) if True, removes Illumina’s internal control probes.

verbose: bool

(default False) reports out on number of probes removed.

a dataframe with samples removed.