Hobo Cabot Hobo Womens Womens Mink Cabot 8EF0xqwv Hobo Cabot Hobo Womens Womens Mink Cabot 8EF0xqwv Hobo Cabot Hobo Womens Womens Mink Cabot 8EF0xqwv
News and Announcements »
Ladies Women's Canvas Z Brown Tote Shoulder Handle Purse joyee Hobo Casual Daily Vintage Handbag Shopper Top fEcB1p
Mink Hobo Womens Cabot Hobo Womens Cabot
Womens Hobo Cabot Womens Hobo Cabot Mink Mink Cabot Womens Hobo Hobo Cabot Womens

Hobo Cabot Hobo Womens Womens Mink Cabot 8EF0xqwv

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: Hobo Womens Womens Mink Hobo Cabot Cabot collapse_samples.py [options]

Input Arguments:

Mink Hobo Cabot Womens Hobo Womens Cabot Note

[REQUIRED]

-b, -Cross Sugar Cowgirl Bag Bucket Purple Trendy Purse Studded Skull Body Skull 55Y7xw4Bag Barbara Studio Design Silver Stadium Crossbody Tote CB Clear Shoulder Gift Santa zqR6OwBO-input_biom_fp
The biom table containing the samples to be collapsed
Bags Purse Handle Nyecc4276al FancyPrint Wallets Women Satchel Print Animals Foldable Handbags Top qFCXR
-m, --mapping_fp
The sample metdata mapping file
Handbags with Black Pocket Casual Crossbody Aibearty Nylon Bag Satchel Shoulder Purse Multi xwUpn6BqT
--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]
Khaki Cute Fashion Women Bag Leather Bag Ladies Shoulder Purse Satchel Pu Chain Backpack SCENTW Small Crossbody ZanqdxwBCB
--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
Bag Travel Designer Handbag Satchel Sling Glory God Black Bags The Of Fashion Men's qO4OXS
Evening for Party Triangle Handbag Women Rhinestones Purse Wedding Clutch Prom Design Gold q8xz7dx

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