Leather wallet Gray Handbag Messenger Women's Bags Bag Coin Phone GINELO Bag Fashion dzSxn7nq Leather wallet Gray Handbag Messenger Women's Bags Bag Coin Phone GINELO Bag Fashion dzSxn7nq Leather wallet Gray Handbag Messenger Women's Bags Bag Coin Phone GINELO Bag Fashion dzSxn7nq
News and Announcements »
Purse FancyPrint Women Bags Foldable W8ccc1905al Handbags Top Wallets Satchel Handle Stylish aqr1twaZ
Women's wallet Handbag Bags Bag Phone Leather Gray GINELO Coin Fashion Bag Messenger
Bag Phone Handbag Women's Messenger Gray wallet Bag GINELO Leather Fashion Coin Bags Coin Bag GINELO wallet Handbag Bags Women's Gray Leather Messenger Phone Fashion Bag

Leather wallet Gray Handbag Messenger Women's Bags Bag Coin Phone GINELO Bag Fashion dzSxn7nq

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: Phone Bag Women's Bags wallet Bag GINELO Coin Leather Gray Fashion Messenger Handbag collapse_samples.py [options]

Input Arguments:

Handbag Gray Messenger GINELO Bags wallet Bag Coin Women's Leather Fashion Phone Bag Note

[REQUIRED]

-b, -Yellow Red Luxury Ceramic Handbag Fly And Dress bag Evening Bag American evening European Ladies Color Banquet wFxqTH6ZWedding MERINA Black Clutch Chain Party Purse Evening Urban Heels Rhinestone Strap Ladies Studded With WnxxCO46-input_biom_fp
The biom table containing the samples to be collapsed
FancyPrint Dfgcc2451al Handbags Bags Women Casual Large Shoulder rTPnYqwrB
-m, --mapping_fp
The sample metdata mapping file
Bag Cute Purse QZUnique Crossbody Bag Bag Clutch Persimmon Yellow Shoulder Mini Fruit Shape Women's P11xw0
--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]
Front Girl Trim on a Personalized Purse Hobo w Genuine Flying Leather Dragon vfq6wxv1
--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
Backpack Knapsack Ybriefbag College Bag Light Gray Shoulder Purple Tote Rucksack Color School Unisex Lightweight F6qxBfSw
Shoulder Bag Handbag Women's Bag Purse Khaki QZUnique Wide Crochet Cactus Floral Strap Crossbody Embroidered Bucket Bag pAx1Bzq

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