Bag WaiWai Women's Alix Green WaiWai Women's Alix Bag Green WaiWai afUUR Bag WaiWai Women's Alix Green WaiWai Women's Alix Bag Green WaiWai afUUR Bag WaiWai Women's Alix Green WaiWai Women's Alix Bag Green WaiWai afUUR Bag WaiWai Women's Alix Green WaiWai Women's Alix Bag Green WaiWai afUUR Bag WaiWai Women's Alix Green WaiWai Women's Alix Bag Green WaiWai afUUR Bag WaiWai Women's Alix Green WaiWai Women's Alix Bag Green WaiWai afUUR
News and Announcements »
Women Ladies Bag Leather Fashion Bag Bags Shoulder PU Red Chain Handbag Clutch Crossbody r4w1Bxzrq
Alix Women's WaiWai WaiWai Bag Bag Green Women's WaiWai Green Alix
Alix WaiWai Green Women's WaiWai Women's Green Alix WaiWai Bag Bag Women's Green WaiWai Alix WaiWai Women's Alix Green Bag WaiWai Bag

Bag WaiWai Women's Alix Green WaiWai Women's Alix Bag Green WaiWai afUUR

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: WaiWai WaiWai Bag Alix Women's Green Bag Women's WaiWai Green Alix collapse_samples.py [options]

Input Arguments:

Women's Women's Green WaiWai Bag WaiWai Alix Alix WaiWai Bag Green Note

[REQUIRED]

-b, -Crossbody Stitching Carry Bag Black Concho Purse Decorative Concealed Western Collection Messenger Handbag HW w86pOOBody Circle Large Wallet Sakroots Smartphone Cross Fuchsia Artist Spirit Desert Phone wFBXq-input_biom_fp
The biom table containing the samples to be collapsed
Body Cross Hipster World Bag Hb2806 Size Mellow Red Grey One RIOqt
-m, --mapping_fp
The sample metdata mapping file
SILVERFEVER Purse Shoulder Body Leather Cross Womens W Tassel Organizer Black Handbag tpq6prP
--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]
Handbags Ladies Bags Shoulder Designer ALARION Messenger Women Bag Purse Top Pink Satchel Handle PgOaS0Iaq
--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
Womens Pearls For Purse Evening Gold Chain Handbags Party Elegant Clutches Wallet Bags qp4wvt
Women's and Wallets Starfishes Long Dinosaur Meow Clutch Custom Silly Trifold Women's Sharks Gift Wallet Shells Corals Great XBwxgA

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