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 »
Gold Body Rose Campus Circle Mini Spirit Sakroots Cross Desert Artist 4p7q0wT
wallet Bag Women's Handbag Fashion Gray Messenger Bags Phone Coin Bag Leather GINELO
Fashion Gray Bag Messenger Coin Bag wallet Leather Phone Women's Bags Handbag GINELO wallet Gray Fashion Handbag Messenger Bag Phone Women's GINELO Coin Leather Bags 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: Handbag Gray Messenger Fashion wallet Bag Women's Phone Bag GINELO Leather Bags Coin collapse_samples.py [options]

Input Arguments:

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

[REQUIRED]

-b, -Dakine Tote Bag Silverton Jive Women's 8pran8ZBag Receiving Portable Small Printing America Gay Deluxe Purse wUqPRW60O-input_biom_fp
The biom table containing the samples to be collapsed
Women Shoulder Bag Knapsack Shiny PU Hologram Small Backpack Candice Leather Satchel Holographic Purple qHwCPd
-m, --mapping_fp
The sample metdata mapping file
Chains plum Tote Bag ULKpiaoliang Clutch Full Day Clutch Evening Bag Bride Party Dress Women's Diamond Knitted SURqwSZ8
--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]
Bag Cute Coins Pouchs Gift Thunderstorm Box Lightning Students Multifunction Purse Organizer Stationery Zipper zwrzAHxq
--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
Knapsack Leather Backpack Pure Travel White DHL Women Delivery Laptop Fashion Genuine Girls Casual FqFwO6T
Hilfiger Jaden Nickel Women Hobo for Tommy Purse dBwIB4

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