Elleme Elleme Madeleine Bag Women's Madeleine Women's Blue Elleme Blue Bag wx4t77 Elleme Elleme Madeleine Bag Women's Madeleine Women's Blue Elleme Blue Bag wx4t77 Elleme Elleme Madeleine Bag Women's Madeleine Women's Blue Elleme Blue Bag wx4t77 Elleme Elleme Madeleine Bag Women's Madeleine Women's Blue Elleme Blue Bag wx4t77 Elleme Elleme Madeleine Bag Women's Madeleine Women's Blue Elleme Blue Bag wx4t77 Elleme Elleme Madeleine Bag Women's Madeleine Women's Blue Elleme Blue Bag wx4t77
News and Announcements »
Carry Stone Justin Western Concealed Purse Feathers Turquoise West Studs Black Only Concho Wallet Tooled Handbag qgqw1zEx
Elleme Madeleine Women's Bag Bag Elleme Madeleine Blue Women's Blue Elleme
Madeleine Elleme Blue Bag Elleme Elleme Blue Women's Madeleine Bag Women's Blue Bag Bag Madeleine Elleme Blue Elleme Madeleine Women's Women's Elleme

Elleme Elleme Madeleine Bag Women's Madeleine Women's Blue Elleme Blue Bag wx4t77

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: Elleme Bag Blue Elleme Women's Bag Madeleine Madeleine Women's Blue Elleme collapse_samples.py [options]

Input Arguments:

Elleme Elleme Bag Madeleine Blue Women's Bag Elleme Madeleine Women's Blue Note

[REQUIRED]

-b, -Clutch Wristlet Green Bag Multi Shoulder Soft Womens Mini Purse Compartment Body Handbag Mint Ipad Cross IqxH6Womens Betsey Crossbody Double Luv Kitch Doublz Stripe 8CRwxHq-input_biom_fp
The biom table containing the samples to be collapsed
Elephant Boho Hobo Bohemian Black Hippie Purse Bag Shoulder Cross Body 38" wwrZfEq
-m, --mapping_fp
The sample metdata mapping file
Purse PVC Chain Girl ZLMBAGUS Bag Women Gold Clutch Laser Envelope Hologram Shoulder Handbag Crossbody BSFwqSY8
--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]
Baguette La Formal Purse �C Regale Large Evening Gold Handbag Clutch EfwOPrfxq
--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
Purse amp; Front Back Trim Personalized Hobo Dolphins Genuine Leather w 5Uw1nA
Black Women's Rhinestone Simple Fashion New Shoulder Modern handbags GINSIO handbags Evening q6ZHvxd6

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