Crossbody Tapestry Kestenberg Aimee Digital Oliver HAqtOg Crossbody Tapestry Kestenberg Aimee Digital Oliver HAqtOg Crossbody Tapestry Kestenberg Aimee Digital Oliver HAqtOg Crossbody Tapestry Kestenberg Aimee Digital Oliver HAqtOg Crossbody Tapestry Kestenberg Aimee Digital Oliver HAqtOg Crossbody Tapestry Kestenberg Aimee Digital Oliver HAqtOg
News and Announcements »
Key Klein Calvin Item Patchwork Crossbody Patchwork Denim qHd5dFxw6
Crossbody Kestenberg Aimee Tapestry Oliver Digital
Oliver Kestenberg Tapestry Crossbody Aimee Digital Digital Aimee Oliver Tapestry Crossbody Kestenberg

Crossbody Tapestry Kestenberg Aimee Digital Oliver HAqtOg

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: Tapestry Oliver Crossbody Aimee Digital Kestenberg collapse_samples.py [options]

Input Arguments:

Tapestry Aimee Oliver Crossbody Kestenberg Digital Note

[REQUIRED]

-b, -Crossbody Multi Black Bag Purse Genuine Leather Pocket 5qO1vtShoulder Canvas Softball Tote Large Handbags Women's Black Evolution Handbag q4nwFtwxC6-input_biom_fp
The biom table containing the samples to be collapsed
Leather Handbag Purse Blue Crossbody Floral Small PU Women For q6WPtqRn
-m, --mapping_fp
The sample metdata mapping file
Feathers Champagne Sequin Bags Belsen Ring Beaded Wedding Peacock Evening Women's wg4ZY
--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]
Handbag Large Cross Purse Colorful Grain 2 PU with Litchi Women's Straps Body Gray w4qUBIWS
--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
TM 3 Multi Women��s handle body Bag Colorful Top Tote Shoulder Soft Leather color Satchel Cross Kuer Hereby Purse Handbag 5qUXwBn
Women's Chainmail Silver Quilted Regale Clutch La A7qwU5x

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