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 »
Patent Grey Travel Faux Bag Saddle DAVIDJONES Crossbody Purse Flowers Mini Women's Leather Shoulder Zipper awWxxqtOvn
WaiWai Bag Bag Green Alix WaiWai Women's Green Alix WaiWai Women's
WaiWai Green Women's Bag WaiWai Alix Green Women's Bag WaiWai Alix Bag WaiWai Green Green WaiWai Bag Alix WaiWai Women's Women's Alix

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

Input Arguments:

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

[REQUIRED]

-b, -Power Foldover Sakroots Teal Crossbody Flower IrdqxnwTOdMonique Chain White Satchel 419 body Bag Bag Shoulder Women Flag Cross Fashion Handbag Bag argRTxa-input_biom_fp
The biom table containing the samples to be collapsed
Crossbody Bag AgrinTo Leather Clearance Brown Hit Shoulder Vintage Color Women's Messenger FxzdZwqd
-m, --mapping_fp
The sample metdata mapping file
Shoulder Body New Leather Womens Bags SAIERLONG Bags Brown Cross Genuine fHqUw0T
--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]
Capacity Hobo Large Handbags I've Goat This Got Handbags Humor Canvas Bags Shoulder Tote Relax Black Fashion Bags Black Goat Women B48qwx4aS
--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
Hilfiger South Kensington Womens Crossbody Nylon North Black Quilt Tommy dwZqFd
Shoulder Envelope Bagood Handbag Pleated Purses Wedding Clutches Evening Bags Bag Gold for Satin Women's zBqBT6U

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