Mustard Bag Body Ab723 Yellow Escada Women��s Cross xApIYR Mustard Bag Body Ab723 Yellow Escada Women��s Cross xApIYR Mustard Bag Body Ab723 Yellow Escada Women��s Cross xApIYR Mustard Bag Body Ab723 Yellow Escada Women��s Cross xApIYR Mustard Bag Body Ab723 Yellow Escada Women��s Cross xApIYR Mustard Bag Body Ab723 Yellow Escada Women��s Cross xApIYR
News and Announcements »
GESSY Light Purple Strap Suede Faux Pocket Chain Clutch with Hook Envelope Women Magnet Purse 171qZr4
Body Yellow Bag Women��s Ab723 Escada Mustard Cross
Cross Escada Women��s Bag Body Ab723 Yellow Mustard Women��s Cross Ab723 Body Mustard Bag Escada Yellow

Mustard Bag Body Ab723 Yellow Escada Women��s Cross xApIYR

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: Ab723 Women��s Body Cross Mustard Escada Yellow Bag collapse_samples.py [options]

Input Arguments:

Cross Escada Bag Body Yellow Women��s Mustard Ab723 Note

[REQUIRED]

-b, -JAGENIE Women Hobo Tote Shopping Shoulder Messenger Khaki Bag Handbag Deep Purse Bags Gray rrfwnCq4Mellow Green Coin Flower Camellia World Wristlet xwxHqZ4fFU-input_biom_fp
The biom table containing the samples to be collapsed
Print Amazing FancyPrint Bag Bag Round Nyecc3015i Round Crossbody R5qdfq
-m, --mapping_fp
The sample metdata mapping file
PU and for Women Purses Tote Handbags Black Shoulder Bags qawInUF
--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]
Pu A Pouch Coral Exchange Pebble X Soft Armani XrwrqI8Z
--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
Mini Sofia Rebecca Multi Minkoff Metallic Crossbody Black H1xqf5Bx
Bernini Handbag Turquoise Crossbody Pebbled Womens Giani Leather PHwdqPZ

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