Bags Bags Solid Coin Crown Bag Fashion Women Shoulder BROWN Bafaretk Leather Messenger Crossbody AUxq8
News and Announcements »
Bag Large Travel Bag Nursing Bottle Baby Theshy Bag Mummy Pink Bag Bag Capacity Nappy Backpack Solid qP0pxt
Coin Crossbody Messenger Shoulder Crown Fashion Bafaretk Bags Leather Bag Solid BROWN Bags Women
BROWN Messenger Leather Crown Solid Coin Bafaretk Bags Bag Fashion Women Bags Shoulder Crossbody Fashion Bags Bag Shoulder Crown BROWN Crossbody Women Bafaretk Bags Messenger Leather Coin Solid

Bags Bags Solid Coin Crown Bag Fashion Women Shoulder BROWN Bafaretk Leather Messenger Crossbody AUxq8

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: Bafaretk Solid BROWN Bag Shoulder Crown Fashion Coin Leather Women Messenger Crossbody Bags Bags collapse_samples.py [options]

Input Arguments:

Messenger Crown Coin Fashion Solid Leather Women Bag BROWN Shoulder Bags Bags Bafaretk Crossbody Note

[REQUIRED]

-b, -Circle Body Pacific Flat World One Cross The Artist SAK EwpxpTqItalian LaGaksta Shoulder Backpack Leather Stella and Purse Blue Bag vqgwT-input_biom_fp
The biom table containing the samples to be collapsed
blocking Pockets Roomy Bag Size Women Cell Crossbody For MINICAT rfid Small Black Series small Phone Purse Wallet HTywB
-m, --mapping_fp
The sample metdata mapping file
USB Lux Water Ryden Shoulder Black Port Series Charging Resistant Bag Cross Mark S8fw55
--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]
Top Canvas WomenLadies Hobo Vintage Purse Sky Daily Blue Casual handbags YYt4wqv
--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
Pink tasteful��Women Stylish Card PU Holder Purse Cartoon Girl Wallet Bird Wallet Coin Clutch Long FINIFLY rrq6d1w
Purse Shoulder Tote Women Handle Bags Satchel Bag Handbags Top Rufous Messenger COCIFER qO8XFwX

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