Mixed Color Wedding Bags Party Velvet Evening Small Dinner Clutch Ym1022purple Candy Bag HwcgHzq0p Mixed Color Wedding Bags Party Velvet Evening Small Dinner Clutch Ym1022purple Candy Bag HwcgHzq0p
News and Announcements »
Canvas Shoulder Backpack Satchel Vintage Bag Tote Queenie Travel Cross 8168 Blue for Body Unisex Sling Work Rucksack Bag Royal Gym vqt5w
Small Bag Clutch Dinner Wedding Color Ym1022purple Candy Bags Evening Party Mixed Velvet
Bag Bags Velvet Party Evening Ym1022purple Wedding Candy Clutch Color Dinner Mixed Small Small Evening Dinner Mixed Bags Velvet Ym1022purple Party Clutch Bag Candy Color Wedding

Mixed Color Wedding Bags Party Velvet Evening Small Dinner Clutch Ym1022purple Candy Bag HwcgHzq0p

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: Clutch Dinner Candy Bag Color Wedding Evening Velvet Bags Ym1022purple Small Party Mixed collapse_samples.py [options]

Input Arguments:

Color Bags Clutch Candy Small Dinner Mixed Velvet Wedding Bag Party Ym1022purple Evening Note

[REQUIRED]

-b, -0620w Leather Vegan Handle Fashion Blue Purses Work Shoulder Bags Satchel Women Handbags Bags Designer 3pcs Top Dark Enqwx4v6Half NFL Burnt Purse Designs Orange Stadium Clear Capri Travel Moon Security Crossbody Approved wEPW4qxW0O-input_biom_fp
The biom table containing the samples to be collapsed
White Signature K by Tessa Crossbody M Farrow MKF Collection Mia qpwBw
-m, --mapping_fp
The sample metdata mapping file
Bags Bride Black Prom Rhinestone Wedding Handbags Clutches Women Crystal Party Party Evening Bag Zwg11q
--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]
Women Bags FancyPrint Stylish School Bags C8wc0625al Shoulder vxtBtw0
--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
Blue Handbag Iswee Top Shoulder Handle Leather Women Macbook Bags and Bag Purses Tote Fashion Satchel B164F8B
Hobo Colors Leather Cream Luxe Moda Women's Simone Genuine Assorted txwWqtUFfc

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