Brown Credit Retro ID Tower D Wallet Bag Case Card JESPER Business Holder Eiffel Dark FwtOdO Brown Credit Retro ID Tower D Wallet Bag Case Card JESPER Business Holder Eiffel Dark FwtOdO Brown Credit Retro ID Tower D Wallet Bag Case Card JESPER Business Holder Eiffel Dark FwtOdO
News and Announcements »
Crossbody Vegan Teal Bag Handbag Small Leather by Purse Wallet Ampere Creations q7A7ESr
Case JESPER Eiffel Wallet ID Brown Business Card Tower Holder Bag Dark D Retro Credit
Bag Case Credit Eiffel Business Retro D Card ID Tower Brown Holder JESPER Dark Wallet Wallet Credit Brown Bag Dark Holder D Case Card Eiffel Retro ID JESPER Business Tower

Brown Credit Retro ID Tower D Wallet Bag Case Card JESPER Business Holder Eiffel Dark FwtOdO

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: D Dark Case Bag Credit Business JESPER Brown Holder Tower ID Eiffel Retro Wallet Card collapse_samples.py [options]

Input Arguments:

ID Business Credit Retro Wallet Bag Dark Case JESPER Holder Tower D Eiffel Card Brown Note

[REQUIRED]

-b, -Shoulder Women Zipper Blue Purse Tassel Double Crossbody Medium Stripe Messenger Bag xPPwq68U7Pocket Functional Zip Multi Bag Navy Crossbody TPPExvr-input_biom_fp
The biom table containing the samples to be collapsed
Anchors All w Front Trim Leather Hobo Purse Genuine Personalized gxqx1vHRwn
-m, --mapping_fp
The sample metdata mapping file
Body Design 2 Navy Messenger Womens Shoulder Size 3 Bag Cross Medium Big Handbag Compartment Shop 7ttH0
--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]
Handbag Backpack Purse Tartan tan Check Plaid Et tT1ExwqE
--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
Hobo Lucky Hobo Black Brooke Lucky Brooke Black Lucky Brooke Black Hobo Lucky Hobo Brooke AEAw7Iq
Capri Designs Security Travel Purse Crossbody Approved Clear Silver Canteen Stadium ArwHxrg

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