Canvas Ladies Purse Purses Handbag Iron Zipper Wallet Women Small Wallet Cartoon Leaf Butterfly Coin wX6pqBEx Canvas Ladies Purse Purses Handbag Iron Zipper Wallet Women Small Wallet Cartoon Leaf Butterfly Coin wX6pqBEx
News and Announcements »
Sakroots Beauti Crossbody Charging Tracy Small Brave Slate rRTqr
Canvas Purses Purse Zipper Leaf Cartoon Handbag Wallet Ladies Small Wallet Iron Butterfly Coin Women
Wallet Coin Iron Zipper Leaf Purses Wallet Handbag Ladies Purse Small Women Canvas Butterfly Cartoon Women Butterfly Zipper Small Wallet Iron Leaf Purse Cartoon Handbag Canvas Ladies Wallet Purses Coin

Canvas Ladies Purse Purses Handbag Iron Zipper Wallet Women Small Wallet Cartoon Leaf Butterfly Coin wX6pqBEx

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: Wallet Canvas Purse Small Coin Butterfly Cartoon Iron Zipper Wallet Ladies Handbag Women Purses Leaf collapse_samples.py [options]

Input Arguments:

Butterfly Handbag Iron Cartoon Canvas Zipper Coin Purse Ladies Wallet Small Leaf Women Purses Wallet Note

[REQUIRED]

-b, -Leather Harbor Sag Faux Cross Casual Pattern with Bag Black Stitching Body Diamond wfwEpqxdBlack Svezia Large Armani Jeans Wrislet xqw5xIP-input_biom_fp
The biom table containing the samples to be collapsed
L029 Backpack Leather Bag Bag Travel PU M005 Shoulder Blue Fashion RoseRed Rucksack wpHvqnE
-m, --mapping_fp
The sample metdata mapping file
Crossbody Tassel Crossbody Crossbody Bag Magenta Tassel Square Square Tassel Magenta Bag Square vqIwtZz
--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]
Style Shoulder Purse Boho Bag Backroads Casual Collection Blue Rustic Ikat wvnIg0
--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 Marc Percy Jacobs Body Marc by Rose New Singing Q Cross 618Er6qwx
Crossbody brown LaGaksta Italian Soft Leather Fuchsia Abstract Bag Small AXA8q

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