Core Module

Core.Stats module

class Core.Stats.Dist(beta_list, sample_id, lab)

class Core.Stats.TopList(samples1, samples2, all_probes)

get()

ttest(samples1, samples2, probe)

class Core.Stats.Transform

class Core.Stats.Ttest(sample1, sample2, probe, diff_id_list)

Bases: threading.Thread

run()

Module contents

class Core.Group(list_of_samples)

Create a new Group groups.

Parameters:list_of_samples – A list of sample objects. Returns:A Group object.

class Core.ParseBatch(folder, delim='t', avg_beta_header='.AVG_Beta')

Parse a series of data in a folder.

Parameters:

• folder – A string that represent a folder.
• delim – delimitation character used in the data file [default = tab].
• avg_beta_header – A string that represents average beta values [default = .AVG_Beta].

Returns:

A ParseBatch object. Use get_samples() function to retrieve sample information.

get_samples()

Return all sample objects created from all files

class Core.ParseConfig

class Core.ParseFile(filename, delim='t', avg_beta_header='.AVG_Beta')

Parse a single file. The file could still have multiple groups. This module automatically finds and parses them.

Parameters:

• filename – A string that represent a data file name.
• delim – delimitation character used in the data file [default = tab].
• avg_beta_header – A string that represents average beta values [default = .AVG_Beta].

Returns:

A ParseFile object. Use get_samples() function to retrieve sample information.

check_file(filename)

Check input filename

Parameters:filename – A string that represents a data file. Returns:A boolean value.

get_samples()

Returns all groups in this file.

class Core.Sample(name=None, probes=None)

Sample data object. Each sample has a name which is a string type and Probe methylation data which is a dictionary type.

Parameters:

• name – Name of the sample.
• probes – methylation data of the sample - in dict type.

Returns:

A Sample object.

Core.get_all_beta(sample)

Get all beta values.

Returns:A list of beta

Core.get_all_sample_name(samples)

Get all sample name.

Returns:A list that contain sample names.

Core.get_genes_from_probes(probe_list)

Get gene names and number of probes associated with each gene.

Parameters:probe_list – A list of probes. Returns:A dictionary of genes names and probes numbers.

Core.get_id_beta(sample)

Get all beta values.

Returns:return beta values of a sample.

Core.get_probe_avg(probe_id, samples, verbose=False)

Get Probe AVG values.

Parameters:probe_id – A list of probe ids. Returns:A list of avg beta values.

Core.get_probes_avg(probe_id_list, sample)

Get probe AVG beta values from a list of probes for all groups

Parameters:probe_id_list – A list of probe ids. Returns:A list of beta values.

Core.get_sample_by_name(samples, sample_name)

Returns a sample by name.

Parameters:sample_name – Sample name, a string. Returns:Return a sample object.

Core.get_sample_by_no(samples, sample_no)

Returns a sample by number [zero based].

Parameters:sample_no – Sample number, a zero based integer. Returns:Return a sample object.

Core.probes_to_bed(filename, probes, sample)

Writes a BED file containing the probe beta info.

Parameters:

• filename – A filename to be stored.
• probes – A list of Probe info.
• sample_no – The sample number to include in the BED file.

Returns:

Static function - stores a file.

Core.samples_to_bed(base_filename, probes, samples)

Return a BED file representative of all groups for the provided probes.

Parameters:

• base_filename – A base name for output file
• probes – A list of probes objects.
• samples – A list of groups to extract data.

Returns:

Static function - stores a file.

Core.write_data(file_name, samples, probes)

Export data to data table

Parameters:

• samples – A list of groups.
• probes – A list of probes.

Returns:

Writes a data file.