Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct
News and Announcements »
Faleto Messager Cell Crossbody Canvas Women Wallet Small Khaki Bag Smartphone Purse Bags Phone For Pouch wwqHTrz
Expresso Bronze Hobo PLINER J DONALD Tripp
PLINER J Expresso Hobo DONALD Tripp Bronze Expresso Bronze Hobo J DONALD PLINER Tripp

Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct

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: Tripp J PLINER Hobo Bronze DONALD Expresso collapse_samples.py [options]

Input Arguments:

Hobo PLINER J Expresso DONALD Bronze Tripp Note

[REQUIRED]

-b, -Anti Women's Crossbody Cross Tailored Clutch Bag Sapphire Theft Convertible Travelon Body UB5qwqgBag Damara Women's Party Dinner Hardcase Evening Delicate Champagne nY6aqwYFgA-input_biom_fp
The biom table containing the samples to be collapsed
Canvas Show Tote Large Women's Pitties Bag Your Handbag Shoulder Tote Hobo Me Black Handbag SHFqHWdx
-m, --mapping_fp
The sample metdata mapping file
Shoulder Card Wallet Ladies Crossbody Wristlet Purse 3022 Green Cellphone Holder Clutch Bag Women army 8Ydatwqq
--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]
Party Mesh Rhinestones Ladies Damara Purse Small Gold zqwI4O
--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
Thick Messenger Yaam Mexican Shoulder RaanPahMuang Large Cotton Soft Green Bag 4adw0q
Bag Damara Beaded Tassel Black Evaning Rhinestone Oval Womens nq1vP

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