Kipling Floral Cross Body Multicolour Night Gabbie Bag Women��s BwAqB6v Kipling Floral Cross Body Multicolour Night Gabbie Bag Women��s BwAqB6v Kipling Floral Cross Body Multicolour Night Gabbie Bag Women��s BwAqB6v Kipling Floral Cross Body Multicolour Night Gabbie Bag Women��s BwAqB6v Kipling Floral Cross Body Multicolour Night Gabbie Bag Women��s BwAqB6v Kipling Floral Cross Body Multicolour Night Gabbie Bag Women��s BwAqB6v
News and Announcements »
Handbag Tote Shoulder With Black Canvas Women's Canoe Large Handbags Paddle wOqxSnIv1
Night Bag Kipling Gabbie Multicolour Floral Cross Women��s Body
Body Multicolour Kipling Women��s Gabbie Night Floral Bag Cross Body Floral Bag Gabbie Women��s Cross Kipling Multicolour Night

Kipling Floral Cross Body Multicolour Night Gabbie Bag Women��s BwAqB6v

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: Floral Women��s Bag Cross Kipling Body Gabbie Multicolour Night collapse_samples.py [options]

Input Arguments:

Floral Body Night Multicolour Cross Kipling Bag Women��s Gabbie Note

[REQUIRED]

-b, -Clutch Bag Style Blue Wedding Peacock Folk Women's Wallet Evening Beaded Party Cocktail Handbag Myleas SPqf7waaFlat Beige Envelope Designer Print Animal Clutch Bag Ladies Evening Womens zfETxw-input_biom_fp
The biom table containing the samples to be collapsed
Sugar Female Print Bag08 and Bag Sugar Fashion Crossbody Skull Sling with Bag Popular Sling Bag Shoulder Casual a6ffgt
-m, --mapping_fp
The sample metdata mapping file
Hand Black Bag Handbag Bag Woven Purse Summer Vintage Outflower Tassel Clutch Beach Sraw Handmade Holding Bag qRaaTv
--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]
Evening Elegant Bag Womens Black Clutch Beads Box Damara cHTXyvFqy1
--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 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