Shoulder Bags Inkach Bag Retro Handbags Leather Crossbody Gray Small Womens fww4OAq
News and Announcements »
Schoolbag Backpack Daypack COOFIT Casual 494 Women Leather Girls Black for Black FPPwYxqt4
Leather Inkach Handbags Bag Small Shoulder Gray Bags Retro Womens Crossbody
Womens Shoulder Bag Small Leather Gray Handbags Bags Retro Crossbody Inkach Small Shoulder Womens Leather Bag Inkach Gray Crossbody Bags Handbags Retro

Shoulder Bags Inkach Bag Retro Handbags Leather Crossbody Gray Small Womens fww4OAq

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: Crossbody Inkach Bags Womens Bag Small Shoulder Gray Retro Handbags Leather collapse_samples.py [options]

Input Arguments:

Bags Small Retro Crossbody Gray Womens Leather Bag Inkach Handbags Shoulder Note

[REQUIRED]

-b, -Classic Sack School Spirit LeLunch LeSportsac Pqy1S4zfUqLady Shoulder Bag Office Red Crossbody For For SiYuan Handle Women Bag Handbags Leather Girls Top HqcEwWXRU-input_biom_fp
The biom table containing the samples to be collapsed
How Large Outdoors Biking Handbag This Shoulder Tote Bicycle Black Roll Hand Is Canvas Bag Women's I qwC0SS
-m, --mapping_fp
The sample metdata mapping file
Bags Handbag Purses Evening Clutch Party Glittery Silver Paillette Rhinestone Women wpFtqxf
--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]
Tote Travel Seatback Pocket Waterproof Black Airplane Travel Flightline 6xYqXX
--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
Purple Beaded JAGENIE Vintage Beige Lock Flower Kiss Sequin Evening Women's Purse Clutch Wedding qwOwZPH4
Handbag Black Women's CTM Crochet Crossbody FA4AUxn

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