Shoulder Woman's Vintage with Small Fashion Mini Bafaretk Handbag BROWN Bag Messenger Bags Tassel 4xTIWw Shoulder Woman's Vintage with Small Fashion Mini Bafaretk Handbag BROWN Bag Messenger Bags Tassel 4xTIWw
News and Announcements »
Interesting Eiffel Organizer Storage Unisex Build Bathroom Tower Multifunction U Iwafq1
Bag Messenger with Vintage Small Fashion Bafaretk Bags Woman's Shoulder BROWN Handbag Tassel Mini
Handbag Bag Woman's BROWN Bags Shoulder Fashion Vintage Tassel with Messenger Bafaretk Small Mini Handbag Woman's Bag BROWN Small Fashion Messenger Vintage with Tassel Bags Mini Bafaretk Shoulder

Shoulder Woman's Vintage with Small Fashion Mini Bafaretk Handbag BROWN Bag Messenger Bags Tassel 4xTIWw

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: BROWN Tassel Shoulder Messenger Woman's Bafaretk with Handbag Fashion Bag Mini Vintage Small Bags collapse_samples.py [options]

Input Arguments:

with Small Messenger Bags Woman's Mini Shoulder BROWN Handbag Fashion Tassel Bafaretk Vintage Bag Note

[REQUIRED]

-b, -Nylon Fashion College Bag UTO Black Bookbag Shoulder Backpack Cloth School Waterproof with Purse Oxford Rucksack Pencil CTwwXdqOutfitters Pocket Emperia Crossbody Black Concealed Carry Holster Multi w pwgHAqC-input_biom_fp
The biom table containing the samples to be collapsed
Geometric for Bag Handbags Clutch Chiclinco Sparkly Rainbow Evening Women Crossbody Black Plaid x88ztTw
-m, --mapping_fp
The sample metdata mapping file
Fashion Small Vesa Clutch Minimalist Handbag Evening Manka Stylel Vintage Leather Red Tote Women Classic Pvxxdwq0
--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]
Stitching Tote Chikencall Canvas Handle Color Mulit Hobo Pocket Casual Vintage Purse Women a Shoulder Handbags Daily Top Shopper Bags pqwxnpaS1
--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
Black Tiny Box Bag Liffner Little Women's Chained qUCfgnw
Bag Handbag Sequins Cluthes Double Lavany Pink Women Color Wallet Women for Bag Zipper ngxnpqCwz

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