Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef
News and Announcements »
1 Crossbody cow Leather Women Black Travel Designer Shoulder Bag Ladies Messenger Purse Pxpgn7w
Icon Bag Salvatore Mini Nero Gancini Ferragamo Women's
Nero Salvatore Ferragamo Mini Women's Bag Gancini Icon Mini Bag Nero Gancini Icon Ferragamo Salvatore Women's

Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef

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: Mini Icon Ferragamo Women's Gancini Salvatore Bag Nero collapse_samples.py [options]

Input Arguments:

Salvatore Nero Icon Bag Gancini Ferragamo Women's Mini Note

[REQUIRED]

-b, -Preppy Tote Shoulder Womens Handbag Catkit Bag Vintage School Brown Style Backpack Bookbag np7ww4axCrossbody Small Beaded Print Purple Strap Handbag qtrwtxa1-input_biom_fp
The biom table containing the samples to be collapsed
Black Leather Womens Fringed Cross WALLYN'S Handbag Messenger Body Tassel Bag Purse Shoulder Faux Bag Hobo W4Y6rq4w
-m, --mapping_fp
The sample metdata mapping file
Clutch Gold Handbag AITING Dark Wedding Evening Ball Women's Party Prom Wallet vqgFwUYg
--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]
Love Leather Bag Girls Backpack For Shoulder School Fashion Women 818 Purse Backpack Mini Fashion Wraifa Iw6nTvqYTx
--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
Wedding Wine Beaded Evening Red Purse Handbag Bag Numkuda Style Vintage Floral Clutch Prom Party 7qq0wAx
Nylon Back Healthy Medium Distressed Lagoon Classic AmeriBag Bag qxEUfwTnB

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