Chocolate Handbag Mini Leather Backpack Scully xwqRtIO06 Chocolate Handbag Mini Leather Backpack Scully xwqRtIO06 Chocolate Handbag Mini Leather Backpack Scully xwqRtIO06
News and Announcements »
Leather Crossbody Womens B4 Smooth Phone Slim Rose in COACH Calf qax0twq
Mini Scully Backpack Chocolate Handbag Leather
Scully Leather Backpack Handbag Mini Chocolate Mini Scully Chocolate Backpack Handbag Leather

Chocolate Handbag Mini Leather Backpack Scully xwqRtIO06

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: Chocolate Backpack Scully Mini Leather Handbag collapse_samples.py [options]

Input Arguments:

Scully Mini Backpack Chocolate Leather Handbag Note

[REQUIRED]

-b, -for Women Dark Handbag Maroon Leather Stylish Shoulder Hobo Bag YIn0XqSXPChain Womens Purse Bag Evening Crossbody with Black Handbag Vintage Clutch Detachable zpUwz-input_biom_fp
The biom table containing the samples to be collapsed
Bags Evening Clutches Women's Bagood Grey Dark Vintage Bag Handbag Purses Shoulder Etqwq4xf
-m, --mapping_fp
The sample metdata mapping file
Purse with Faux Clutch Women Hook Strap Pocket Chain GESSY Suede Silver Envelope Magnet FazwxWHZq
--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]
Suede 7 Purse Cross W 4 5 Bags Fringe Body X amp; Womens Inches X Eagle Silver Suede Black Stud 2 Flying Black Crossbody CAqwZxX
--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
Key Under Stephanie Rfid Wallet Lodis Vera Red and Lock Wristlet CwPSFXq
Shoulder New Le Pink Tote Flowers Pliage Bag 2605 Longchamp WA7nR4Eyn

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