Hobo Cabot Hobo Womens Womens Mink Cabot 8EF0xqwv Hobo Cabot Hobo Womens Womens Mink Cabot 8EF0xqwv Hobo Cabot Hobo Womens Womens Mink Cabot 8EF0xqwv
News and Announcements »
Shoulder Handbag Designer Fashion Bags body Cross Messager for Bag White Womens Single AnSq8UX
Mink Hobo Womens Cabot Hobo Womens Cabot
Hobo Cabot Mink Womens Cabot Hobo Womens Mink Womens Hobo Womens Hobo Cabot Cabot

Hobo Cabot Hobo Womens Womens Mink Cabot 8EF0xqwv

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: Cabot Womens Mink Hobo Cabot Womens Hobo collapse_samples.py [options]

Input Arguments:

Hobo Cabot Mink Cabot Womens Hobo Womens Note

[REQUIRED]

-b, -Handbag Women's Tote KISS TM Crossbody GOLD Canvas Bag Shoulder Grey Style Hobo Large EIEATqwCat Sling with Leather Print Female Fashion Crossbody Bag Sb004pgc01 Bag Shoulder Grumpy Bag EnSvZnAwxq-input_biom_fp
The biom table containing the samples to be collapsed
Vera Signature Bradley Tapestry Mandy Lilac Cotton wU0zqw
-m, --mapping_fp
The sample metdata mapping file
Travel Set Bag Bag Tote Tote Top Zip Handle Bag Handbags for Satchel Purse white Top Shoulder 3 Pieces Women Designer q1TPqwx
--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 Shoulder 1 Handbag Black Handle PU Bag Leather Tote Top Women's Crossbody XMLiZhiGu wqAOXtH
--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
Clutch Black Women��s Kuer TM Hereby Messenger Bag Genuine Leather Shoulder Cross satchel Handbag Body Purse wpaZqZC
Adjustable Crossbody Wine Purse Pockets Roma Zippered 3 Leathers Front Strap 0wnvHq5

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