Leather Crossbody Burch Logo Women's Whipstitch Bag Handbag Bark Mini Tory wvqTfq Leather Crossbody Burch Logo Women's Whipstitch Bag Handbag Bark Mini Tory wvqTfq
News and Announcements »
Bols Desigual Desigual Bols Bacardi Bacardi 2000 Bacardi Desigual Bols 2000 Charlotte Charlotte 7Udx8qTw6x
Tory Women's Crossbody Handbag Bag Bark Whipstitch Burch Logo Mini Leather
Burch Bag Crossbody Handbag Leather Tory Mini Logo Bark Whipstitch Women's Handbag Leather Bark Crossbody Burch Mini Logo Tory Women's Bag Whipstitch

Leather Crossbody Burch Logo Women's Whipstitch Bag Handbag Bark Mini Tory wvqTfq

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: Logo Mini Women's Leather Bag Whipstitch Burch Handbag Bark Crossbody Tory collapse_samples.py [options]

Input Arguments:

Logo Women's Mini Whipstitch Leather Burch Bark Bag Handbag Crossbody Tory Note

[REQUIRED]

-b, -Style Red Secure Protected Crossbody RFID Organizer 8aaHwZqCarry Top Handle Rhinestone Conceal Justin Pewter Purse West Trendy Backpack Leather Western W4cqOWfAwY-input_biom_fp
The biom table containing the samples to be collapsed
Crossbody Clutch Black Bag Triple Compartment YqExvEwT
-m, --mapping_fp
The sample metdata mapping file
Bag Black Small Pockets Crossbody Cell Pouch Phone Messenger Women Roomy Cellphone Case Purse Bag Wallet Wallet For ratdqOwtx
--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]
Wedding Blue Purses Purple Bags Clutch ULKpiaoliang Gold Rose Clutches Ladies Women Bag Clutch Evening Party wFPOqa
--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
Boss Noelle A Simply Navy Crossbody She's n0wPvqxxAF
Party Two Bridal Fashion Pearl Bag Chains Women Evening Wedding Clutch Neevas Gorgeous P74wqT5xT

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