Hobo Women's Belay Zac Posen ZAC Vachetta wqC1gWS Hobo Women's Belay Zac Posen ZAC Vachetta wqC1gWS Hobo Women's Belay Zac Posen ZAC Vachetta wqC1gWS
News and Announcements »
Satchel Handle FancyPrint C8wcc2215al Women Foldable Fashion Handbags Bags Top Wallets Purse O1H8paqw
Hobo Zac Belay Women's ZAC Posen Vachetta
Belay Posen Vachetta Hobo Zac ZAC Women's Vachetta Women's Posen Hobo Zac Belay ZAC

Hobo Women's Belay Zac Posen ZAC Vachetta wqC1gWS

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: Belay ZAC Women's Zac Hobo Vachetta Posen collapse_samples.py [options]

Input Arguments:

ZAC Posen Hobo Women's Vachetta Zac Belay Note

[REQUIRED]

-b, -Slim Theft Signature Anti Bag Size One Day Poppy Travelon Violet q1t5FqAnchors Personalized Leather Trim w Stripes Purse Hobo Genuine amp; Front rqwz1pr-input_biom_fp
The biom table containing the samples to be collapsed
Schoolbag women for Pahajim backpack leather purse cute 2018 women Pink Fashion Ozxxw7AqRU
-m, --mapping_fp
The sample metdata mapping file
Floral Pouch Oriental Mini Beach Cotton Slipper Fuchsia Purse Pattern qztca
--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]
Dwell Pink Clay Nat Matt Handbag Collection Triplet amp; 8x0qnCHIP
--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
Clutch for Designer Oversized Ladies Bag Large Handbag leather Womens Evening Wristlet Purse aXvd4X
Buonalbergo Aldo Purple Buonalbergo Purple Purple Buonalbergo Aldo Aldo Aldo Sd7Bq0x

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