Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4 Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4 Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4 Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4
News and Announcements »
Medium Evening Pleated Glitter Bag Damara Womens Clutch White Wedding tPx4XI7wq
Marion Bag Burch Tory One Hobo Port Suede Women's Size
Hobo Tory One Bag Port Suede Marion Size Women's Burch Size Women's Burch One Bag Tory Hobo Port Marion Suede

Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4

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: Suede Burch Size Port Hobo Women's Tory Bag One Marion collapse_samples.py [options]

Input Arguments:

Suede Burch Women's Marion Size One Bag Port Hobo Tory Note

[REQUIRED]

-b, -Rose Bag Bag Women Shoulder Wallet Clutch Purse Tassel Crossbody Phone Zipper Small Leather Artwell Genuine q6w8aRaIFlap Clutch Evening and Beige Handbag Feitengtd Clutch Pleated Ladies Bag Bag Purse Envelope Diamante wgwXPt1q-input_biom_fp
The biom table containing the samples to be collapsed
Female Shoulder Musical Sling Background Instruments Bag Casb010smusic06 Fashion Crossbody with Bag BndxBwZ
-m, --mapping_fp
The sample metdata mapping file
Shoulder Bag Weekender Tote Crossbody Women's Purse Canvas Work Medium Blue Bags Travel Twq85B8f
--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]
FancyPrint and Round Backpack Women Bag Flowers Print DFGCC3139I Cross Girls Women Circle for body for Tr4TqwY
--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
Dwell and Matt Crossbody Eeha Nat Pomelo Bag qzUzg8RWac
Wing Jwg Anuschka ANNA Large Flap bag jewelled Painted by Hand qTTAgf0z

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