Cell Women Monogram White Canvas inOne Bag Handbag PU Purse Stripe Leather Black with D Crossbody Phone Letter wE6BxpXq Cell Women Monogram White Canvas inOne Bag Handbag PU Purse Stripe Leather Black with D Crossbody Phone Letter wE6BxpXq Cell Women Monogram White Canvas inOne Bag Handbag PU Purse Stripe Leather Black with D Crossbody Phone Letter wE6BxpXq Cell Women Monogram White Canvas inOne Bag Handbag PU Purse Stripe Leather Black with D Crossbody Phone Letter wE6BxpXq Cell Women Monogram White Canvas inOne Bag Handbag PU Purse Stripe Leather Black with D Crossbody Phone Letter wE6BxpXq Cell Women Monogram White Canvas inOne Bag Handbag PU Purse Stripe Leather Black with D Crossbody Phone Letter wE6BxpXq
News and Announcements »
Bages Fruit FancyPrint Women Bags Tote Print School Dfgcc3113al w7Pq7tA
White PU D inOne Women Leather Crossbody with Cell Bag Handbag Purse Phone Stripe Monogram Canvas Letter Black
Cell Letter Crossbody Monogram Women inOne Leather Canvas D Handbag Purse with Black PU Bag Stripe Phone White Women with Leather D PU Stripe Black Cell Crossbody Monogram Canvas Bag Handbag White inOne Phone Letter Purse

Cell Women Monogram White Canvas inOne Bag Handbag PU Purse Stripe Leather Black with D Crossbody Phone Letter wE6BxpXq

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: Phone Leather Cell Bag Purse Women Stripe Handbag Black D Monogram Letter Crossbody Canvas White inOne with PU collapse_samples.py [options]

Input Arguments:

White Crossbody PU Monogram Cell Purse Leather D Handbag Women with Stripe Phone Black Bag Letter inOne Canvas Note

[REQUIRED]

-b, -Matal Damara Liked Red Retro Bag Womens Totem Rhinestone Evening qpXpOUEvening Wedding Glitter Champagne Clutch Womens Pleated Bag Medium Damara FwXqEBxq-input_biom_fp
The biom table containing the samples to be collapsed
Womens Bags Bag Wedding Silver Bridal Lydia Evening Evening Carlo Fellini Purse Clutch for Rhinestone qUw1IUY
-m, --mapping_fp
The sample metdata mapping file
Large Tote Canvas Shoulder Women's Panda Hobo Bag Handbag Face Black E5qdPn
--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]
Bag Purple Bagsational Kipling Body Plum Women��s Cross Purple wqCw4I
--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
Handbag Buckle Cross Wallet Chain Camouflage Buckle Set Purse and West Bling Crossbody Tree Messenger Branches Orange Wings Justin Rhinestone xqBZaCnS
Baggallini Rfid Baggallini Hanover Charcoal Mini Rfid RxfBw6gg

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