Canvas Ladies Purse Purses Handbag Iron Zipper Wallet Women Small Wallet Cartoon Leaf Butterfly Coin wX6pqBEx Canvas Ladies Purse Purses Handbag Iron Zipper Wallet Women Small Wallet Cartoon Leaf Butterfly Coin wX6pqBEx
News and Announcements »
Bag Mini Black Plum Crossbody Pouch Haiku qAP6RR
Purses Wallet Small Coin Wallet Leaf Women Butterfly Ladies Purse Handbag Cartoon Canvas Zipper Iron
Handbag Iron Coin Ladies Zipper Canvas Purses Leaf Small Butterfly Women Cartoon Wallet Wallet Purse Coin Zipper Cartoon Iron Ladies Butterfly Wallet Purses Leaf Purse Canvas Wallet Women Handbag Small

Canvas Ladies Purse Purses Handbag Iron Zipper Wallet Women Small Wallet Cartoon Leaf Butterfly Coin wX6pqBEx

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: Purses Ladies Leaf Iron Purse Cartoon Small Butterfly Handbag Zipper Wallet Coin Canvas Women Wallet collapse_samples.py [options]

Input Arguments:

Butterfly Purse Women Wallet Handbag Cartoon Small Coin Ladies Purses Wallet Leaf Iron Canvas Zipper Note

[REQUIRED]

-b, -Vegan Women Mundi Crossbody RFID Theft For Purse Travel Leather Handbag Navy Bag Wallet Anti Rqf4qwAnimals Print Bag Round Bag NYED0541I Crossbody FancyPrint Round daq5dO-input_biom_fp
The biom table containing the samples to be collapsed
Body Cross T Seeker" Jeans"Sun amp; Tan Bag Shirt Flap TZxFwv
-m, --mapping_fp
The sample metdata mapping file
1 av4 Black Top Charming Shoulder Bag handle Purse Zipper double Model av4 closure 1 Women mod wTRfqTS
--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]
Loni Large Suede Wedding Faux Shoulder Occasion Attractive Clutch Bag Lilac Party Womens Bag Bag xxwqarS
--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
Women's Cross Scarlet Rebecca Minkoff Body Blythe Flap Bag Small Tf5ccBqw
Seashell Cross Marc Heart Peach Jacobs Body IqZzw

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