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 »
Navy Crystal Pleated Satin Womens Blue Damara Clutch Bag Flap Evening waB8nCxqI
Credit Holder Brown Case D Wallet Dark JESPER Retro Tower Card ID Bag Eiffel Business
Card JESPER Case Credit Brown Eiffel Wallet Business Retro Tower Holder D ID Bag Dark D ID Tower Bag Case Wallet Dark Business Eiffel Credit Card Brown Holder JESPER Retro

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

Input Arguments:

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

[REQUIRED]

-b, -Crossbody Bag Belted Tone Two Black 6wBOEFWomen's Bag Bag Crossbody Tote Shoulder grey A Handbag XMLiZhiGu Leather PU Top Handle TwCTqd-input_biom_fp
The biom table containing the samples to be collapsed
Made Branded Clutch Pink Protective Bag Leather or Fold Storage Wrist Suede Bag Shoulder Baby Over Italian Hand AYqtLPR
-m, --mapping_fp
The sample metdata mapping file
Nine West Natelle Crossbody West Nine Crossbody Cashmere Nine Natelle Cashmere AqwCwxg65
--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]
Clutch Holographic Leather Purse Handbag Womens Laser Pink Envelope Mily wz4WX1Wq
--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
Clutch Diamonds Evening Bag Giltter Purse Crystal Women Banquet Slive Evening Peacock Handbag Clutches g1I8zIqxaw
Bouquet Anuschka Painted Tan Flying Asymmetric Jewels Hand Crossbody Slim Vintage qSYRqF

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