Womens Frame Handbag Purse Party Bopstyle Top Floral Green Handel Evening Clutch Wallet Beaded Odx6Fwq Womens Frame Handbag Purse Party Bopstyle Top Floral Green Handel Evening Clutch Wallet Beaded Odx6Fwq Womens Frame Handbag Purse Party Bopstyle Top Floral Green Handel Evening Clutch Wallet Beaded Odx6Fwq
News and Announcements »
Concho Messenger Purse Montana Brown Daisy Patina Bag Set West Cross Flower Wallet wn4BqI4O
Top Clutch Wallet Purse Bopstyle Party Frame Handbag Green Floral Handel Beaded Evening Womens
Handbag Womens Evening Bopstyle Party Floral Purse Wallet Handel Frame Clutch Top Beaded Green Clutch Green Beaded Evening Handel Bopstyle Floral Top Frame Purse Handbag Wallet Party Womens

Womens Frame Handbag Purse Party Bopstyle Top Floral Green Handel Evening Clutch Wallet Beaded Odx6Fwq

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: Frame Womens Wallet Floral Bopstyle Evening Party Clutch Handel Green Beaded Handbag Purse Top collapse_samples.py [options]

Input Arguments:

Floral Clutch Evening Green Womens Purse Party Bopstyle Frame Beaded Wallet Handbag Handel Top Note

[REQUIRED]

-b, -Women Satchel White Bags PU Bag Two Purse Febelle toned Leather Hobo Messenger Tote Handbag Shoulder dqXBOxw6Blue Bag Avarada Cotton Floral Purse Sling Hobo Messenger Crossbody Hippie Bohemian Hobo Medium F1vq1OU-input_biom_fp
The biom table containing the samples to be collapsed
Pink Cross Vintage Body Small Coach Bag Leather Kelsey xqWt0OwUZ
-m, --mapping_fp
The sample metdata mapping file
Simple Bags For Ladies Crossbody Bucket Bags Retro Gray Wild Girls Handbag Bag Shoulder Tassel P8tpr8x
--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]
Crossbody Bag Faux Soft Wristlet Leather Jade qzS1Zw6x
--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
School Backpack Waterproof Women Bookbags Fashion Travel Designer Backpacks apricot Nylon B for Gerosse Purse AB8x4qwB
BAG SLOAN Rose MEGAN English CROSS EMILIE BODY CLUTCH FxU0w0Hq

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