genetest.phenotypes package¶

Submodules¶

genetest.phenotypes.core module¶

class genetest.phenotypes.core.PhenotypesContainer[source]¶

Bases: object

close()[source]¶

get_nb_samples()[source]¶

Returns the number of samples.

Returns:	The number of samples.
Return type:	int

get_nb_variables()[source]¶

Returns the number of variables.

Returns:	The number of variables.
Return type:	int

get_phenotypes(li=None)[source]¶

Returns a dataframe of phenotypes.

Parameters:	li (list) – A list of phenotypes to extract (default: None means all phenotypes).
Returns:	A dataframe containing the phenotypes (with the sample IDs as index).
Return type:	pandas.DataFrame

get_sex()[source]¶

Returns the sex for all samples.

Returns:	The sex for all samples.
Return type:	pandas.Series

is_repeated()[source]¶

Check if the phenotypes contain repeated measurements.

Returns:	`True` if the data contains repeated measurements, `False` otherwise.
Return type:	bool

keep_samples(keep)[source]¶

Keeps only a subset of samples.

Parameters:	keep (list) – The list of samples to keep.

genetest.phenotypes.text module¶

class genetest.phenotypes.text.TextPhenotypes(filename, sample_column='sample', field_separator='t', missing_values=None, repeated_measurements=False, keep_sample_column=False, sex_column=None)[source]¶

Bases: genetest.phenotypes.core.PhenotypesContainer

Instantiate a new TextPhenotypes object.

Parameters:

filename (str) – The name of the text file containing the phenotypes.
sample_column (str) – The name of the column containing the sample identification number (to fit with the genotypes).
field_separator (str) – The field separator (default is tabulation).
missing_values (str or list or dict) – The missing value(s).
repeated_measurements (bool) – Are the data containing repeated measurements (e.g. for MixedLM).
sex_column (str) – The name of the column containing the sex for each sample.

close()[source]¶