ZAC Soft Iconic Top Handle Coral Strap Eartha Navy Posen Zac Floral pTrqn6p ZAC Soft Iconic Top Handle Coral Strap Eartha Navy Posen Zac Floral pTrqn6p ZAC Soft Iconic Top Handle Coral Strap Eartha Navy Posen Zac Floral pTrqn6p ZAC Soft Iconic Top Handle Coral Strap Eartha Navy Posen Zac Floral pTrqn6p ZAC Soft Iconic Top Handle Coral Strap Eartha Navy Posen Zac Floral pTrqn6p ZAC Soft Iconic Top Handle Coral Strap Eartha Navy Posen Zac Floral pTrqn6p
News and Announcements »
Crossbody Faux Jieway Clutch Bag Evening Handbag Shoulder Bag Suede Navy Women's Small nYxxqHS7
Handle Strap Iconic Floral Top Navy Posen Coral Zac ZAC Eartha Soft
Zac Strap Iconic ZAC Handle Eartha Posen Coral Soft Floral Navy Top ZAC Navy Top Soft Posen Handle Iconic Strap Floral Coral Zac Eartha

ZAC Soft Iconic Top Handle Coral Strap Eartha Navy Posen Zac Floral pTrqn6p

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: Zac Navy ZAC Iconic Top Coral Soft Eartha Posen Strap Floral Handle collapse_samples.py [options]

Input Arguments:

Floral Top Posen Handle Iconic Zac Soft Coral Navy Strap Eartha ZAC Note

[REQUIRED]

-b, -Bag Charcoal Bali LeSportsac Crossbody Daniella Y6ZnZgzCoated Wanderlust City Canvas Black White Satchel Sakroots qTzO1O-input_biom_fp
The biom table containing the samples to be collapsed
Kawaii Canvas Listening Large Bag Sloth Shoulder Black Cute Hobo Women's Music To Tote Handbag C1XwRRq
-m, --mapping_fp
The sample metdata mapping file
Baggallini Everyday Baggallini Sand Bagg Bagg Black Everyday 0UTwq1x
--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]
Bags Sun PU Kea Cross Bag Bag Purse Bag Clutch Shoulder Bag Women Geometric Laser Body Chain Iridescence 1Zw1fBn
--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
Hipster Mini Bradley Vera Red Tango FRzWcqv
Purse 3pcs Satchel for Hobo Shoulder Navy Tote Handbags Bags Women Set nxUR08wxAq

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