handbag Britten Tory Leather Chain Solarium Crossbody 39055 Women's Clutch Burch PqF4R handbag Britten Tory Leather Chain Solarium Crossbody 39055 Women's Clutch Burch PqF4R
News and Announcements »
Tote Faux Leather Purse Embossing Blue Shoulder Handbag Patent Satchel Bag Crossbody Lady Glossy ZLMBAGUS wqExFaX4R
Leather Chain handbag 39055 Crossbody Tory Clutch Women's Solarium Burch Britten
Women's Britten Chain Solarium Crossbody Burch 39055 handbag Tory Leather Clutch Burch handbag Women's 39055 Solarium Crossbody Leather Britten Clutch Tory Chain

handbag Britten Tory Leather Chain Solarium Crossbody 39055 Women's Clutch Burch PqF4R

Description:

Collapse samples in a BIOM table and mapping file. Values in the BIOM table are collapsed in one of several different ways; see the available options for –collapse_mode. Values in the mapping file are collapsed by grouping the values if they differ for the grouped samples, and by providing the single value if they don’t differ for the grouped samples.

Usage: Chain Clutch Tory handbag 39055 Crossbody Burch Women's Leather Solarium Britten collapse_samples.py [options]

Input Arguments:

Women's Solarium Burch Leather Crossbody handbag Tory 39055 Clutch Chain Britten Note

[REQUIRED]

-b, -RoseRed Stunning Bags Purse Cocktail Women Handbag Evening For Party Rhinestone Clutch Clutches Crossbody vxYBv7q�C Sales Tote Canvas All Flamingo Chic Bag Anghel Tote Purse Shopping School Bag Carry Canvas bag or Beach by Hobo Bag aazTRxqw5-input_biom_fp
The biom table containing the samples to be collapsed
Womens Bag Clutch Essex Glam Glitter Evening Glitter Purse Navy Sparkly 51xpZqxw
-m, --mapping_fp
The sample metdata mapping file
Exchange Noble Signature Messenger NX Wristlet Crossbody Bag JP Purse Clutch Ivory Beige qAE5xORw
--output_biom_fp
Path where collapsed biom table should be written
--output_mapping_fp
Path where collapsed mapping file should be written
--collapse_fields
Comma-separated list of fields to collapse on

[OPTIONAL]

--collapse_mode
The mechanism for collapsing counts within groups; valid options are: mean, sum, random, median, first. [default: sum]
Chain Gold Handbag Evening Party Bag For Banquet Glitter Women Girls Bag Clutches Shoulder Wedding Women Bag 7wqZxC4S1
--normalize
Normalize observation counts to relative abundances, so the counts within each sample sum to 1.0. [default: False]

Output:

A collapsed mapping file and BIOM table will be generated at the requested paths.

Collapse samples in biom table and mapping file:

Collapse samples by taking the median value for each observation in each group, where group is defined by having the same values for subject in the mapping file.

collapse_samples.py -b table.biom -m map.txt --output_biom_fp collapsed.biom --output_mapping_fp collapsed_map.txt --collapse_mode median --collapse_fields subject
Plum Cross Bossi Nino Daniela Body YqIdPwE
Cerise Hobo Elliott Lucca Bucket Bag Almond qUA5Pw5tWx

Collapse samples in biom table and mapping file:

Collapse samples by taking the median value for each observation in each group, where group is defined by having the same values for both subject and replicate-group in the mapping file.

collapse_samples.py -b table.biom -m map.txt --output_biom_fp collapsed.biom --output_mapping_fp collapsed_map.txt --collapse_mode median --collapse_fields replicate-group,subject

Collapse samples in biom table and mapping file, and normalize the table:

Collapse samples by taking the median value for each observation in each group, where group is defined by having the same values for both subject and replicate-group in the mapping file. Then, normalize the counts to relative abundances, so that the sum of counts per sample is 1.0.

collapse_samples.py -b table.biom -m map.txt --output_biom_fp collapsed-normed.biom --output_mapping_fp collapsed_map.txt --collapse_mode median --collapse_fields replicate-group,subject --normalize