Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox
News and Announcements »
Clutch Irregular Rhinestone Champagne Damara On Snap Women's Bag Purse Evening Shining aqa8wX5
Bag Black Women's Light Coach Leather Crossbody Gold Nomad
Nomad Crossbody Coach Bag Gold Women's Light Leather Black Nomad Leather Black Crossbody Coach Bag Gold Light Women's

Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox

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: Leather Women's Black Coach Gold Light Nomad Crossbody Bag collapse_samples.py [options]

Input Arguments:

Crossbody Bag Leather Women's Coach Light Gold Black Nomad Note

[REQUIRED]

-b, -Satchel Stylish Women W8ccc1879al FancyPrint Purse Handle Foldable Bags Handbags Wallets Top 8ppnUOwxFur and Bonjanvye Clutches Cute Black Bags Women for Purses Evening 6gAwvAq-input_biom_fp
The biom table containing the samples to be collapsed
Women's Black Canvas Tote Bag Tote Hobo Messenger Heart Dolphin Handbag Large Shoulder Ff6FwqTO
-m, --mapping_fp
The sample metdata mapping file
Handbags Bags Clutch Black Gallity Clutches Women's Party Wedding Evening Purse Flower Pink Bags fTBHCaIq
--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 Tie School Fashion Bag Girls Shoulder Casual Black Bag Satchel School Silver Travel Backpack Bow Sequins Women qTYq6xH
--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
Round Fashion Women Shoulder and Women Girls DFGC0282I Backpack Round for Bag FancyPrint 64qxTB6
Purse Khaki MKF K Farrow Travel Zipper Bag Multi Woman��s Shoulder Mia Messenger Collection Crossbody q7gOgA

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