xyalign.ploidy module

xyalign.ploidy.permutation_test_chromosomes(data_frame, first_chrom, second_chrom, chrom_column, value_column, num_perms, output_file=None)[source]

Runs a permutation test comparing mean values of two chromosomes.

Parameters:

data_frame : pandas dataframe

first_chrom : str

The name of the first chromosome in comparison

second_chrom : str

The name of the second chromosome in comparison

chrom_column : str

The name of the column containing chromosome names

value_column : str

The name of the column containing the value of interest

num_perms : int

The number of permutations to use

output_file : {str, None}

If not None, will print results to this file

Returns:

tuple

(mean of first chrom, mean of second chrom, p-value)

xyalign.ploidy.ks_two_sample(data_frame, first_chrom, second_chrom, chrom_column, value_column, output_file=None)[source]

Runs a Two-sample Kolmogorov-Smirnov test

Parameters:

data_frame : pandas dataframe

first_chrom : str

The name of the first chromosome in comparison

second_chrom : str

The name of the second chromosome in comparison

chrom_column : str

The name of the column containing chromosome names

value_column : str

The name of the column containing the value of interest

output_file : {str, None}

If not None, will print results to this file.

Returns:

tuple

(ks_statistic, ks_pvalue)

xyalign.ploidy.bootstrap(data_frame, first_chrom, second_chrom, chrom_column, value_column, num_reps, output_file=None)[source]

Bootstraps the 95 percent confidence interval of the mean ratio of measure for two chromosomes (chrom1 / chrom2).

Parameters:

data_frame : pandas dataframe

first_chrom : str

The name of the first chromosome in comparison

second_chrom : str

The name of the second chromosome in comparison

chrom_column : str

The name of the column containing chromosome names

value_column : str

The name of the column containing the value of interest

num_reps : int

The number of bootstrap replicates to use

output_file : {str, None}

If not None, will print results to this file.

Returns:

tuple

(mean ratio, 0.025 percentile, 0.975 percentile)