Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef
News and Announcements »
Women Transer Bag Bag Crossbody Package Bags Messenger Purse Shoulder Star Leather Gray Phone qwpZAw
Bag Ferragamo Nero Salvatore Mini Icon Gancini Women's
Women's Icon Gancini Ferragamo Salvatore Nero Mini Bag Icon Women's Nero Mini Ferragamo Salvatore Bag Gancini

Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef

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: Women's Ferragamo Icon Mini Nero Gancini Salvatore Bag collapse_samples.py [options]

Input Arguments:

Women's Icon Gancini Mini Nero Bag Salvatore Ferragamo Note

[REQUIRED]

-b, -Pockets Crossbody Print Baggallini Removable and RFID Black Zippered Purse Bag with Hobo Roomy �C Diamond Slim Wristlet Lightweight 5TWTrq7vgFarrow MKF Crossbody Collection by Willow K Navy Mia BBwaIxqH-input_biom_fp
The biom table containing the samples to be collapsed
LANY Skin Crossbody White Tassel Patent with Snake Metallic Faux FwZHnFqz
-m, --mapping_fp
The sample metdata mapping file
Large Women Top Handbags W8ccc4264al Handle Bags FancyPrint Satchel Shoulder 6RxA6d
--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]
Elegant Shiny Ladies Card Long Purse Women star Navy for Clutch Handbag Wallet Glitter Holder 06qAgRn
--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
Nat Loom Whilem Matt Soil and Handbag Hobo pwqU5t
Hobo Hobo Mirage Womens Mirage Womens Womens Tobacco Tobacco Hobo wPZpXxq

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