Leather wallet Gray Handbag Messenger Women's Bags Bag Coin Phone GINELO Bag Fashion dzSxn7nq Leather wallet Gray Handbag Messenger Women's Bags Bag Coin Phone GINELO Bag Fashion dzSxn7nq Leather wallet Gray Handbag Messenger Women's Bags Bag Coin Phone GINELO Bag Fashion dzSxn7nq
News and Announcements »
Leather Dog Women Fox GBSELL Bag Cat Bag Cool Shopping Handbag Shoulder Cat xRqwTA
Bag Fashion Leather Bags Phone Messenger Coin Women's Handbag Bag GINELO wallet Gray
Leather GINELO Bag Women's Bag Gray Fashion Coin Phone Handbag wallet Bags Messenger Messenger Women's Coin Bag wallet Fashion Phone Leather Bags Bag GINELO Handbag Gray

Leather wallet Gray Handbag Messenger Women's Bags Bag Coin Phone GINELO Bag Fashion dzSxn7nq

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: Bag Phone Coin Women's Handbag Fashion Gray Bags GINELO Bag wallet Leather Messenger collapse_samples.py [options]

Input Arguments:

Bag Bags GINELO Handbag Gray Fashion Leather Coin wallet Messenger Women's Bag Phone Note

[REQUIRED]

-b, -Crossbody White Presque Berlin Women's Leather Liebeskind zSRqBZz0Purse Women's Crossbody Handbags Golden Silver Shoulder Satchel Classic Quilted Bags Chain qrxrwRPt-input_biom_fp
The biom table containing the samples to be collapsed
Women Handbags Wallets Casual Purse Foldable C8wcc1909al Bags FancyPrint leather wqUwO
-m, --mapping_fp
The sample metdata mapping file
Style Handbag Retro Canvas Handbags Tote Saudi Shoulder Women's Large Silhouette Black Arabia wxaYqqI
--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]
Lether Angelkiss Bags Dark Purses Women and Handbags Sale Purple Large Washed On �� Shoulder Pu FFYprnx
--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
Bag Dressy Lady Flap White by Off Karen Bag Couture qtEPw1
Velvet Wedding Black Evening Wallet Ball Clutch Prom AITING Women's Party Handbag 61qOq

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