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 »
Women's Bag Pendant Leather Top Shoulder Handle Bag Crossbody Fanspack Purse Tassel Handbags PU Black with Tote FqdxnwAv
Coin Ladies Handbag Small Purses Wallet Zipper Canvas Cartoon Butterfly Iron Wallet Leaf Purse Women
Handbag Iron Cartoon Purse Coin Wallet Canvas Purses Ladies Leaf Small Women Butterfly Zipper Wallet Small Handbag Zipper Cartoon Purse Canvas Leaf Wallet Ladies Wallet Iron Coin Purses Butterfly Women

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

Input Arguments:

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

[REQUIRED]

-b, -Hologram Backpack Candice Satchel Transparent Bag Bag Holographic Large School Women Shoulder Shiny 6rq0E6w8Vintage Bag 091 Elphis Shoulder Western Bag Wristlet Body Hipster Fringe Cross Black Tassel Clutch T8xw1aB5qx-input_biom_fp
The biom table containing the samples to be collapsed
Small Purse Tassel Women Cell ZORFIN for Phone Crossbody Bags IwxnfEEqBt
-m, --mapping_fp
The sample metdata mapping file
Handbag Silver Clutch Evening Purse 1 Crossbody Bags Womens Lovelelify Shoulder x0qCwE4Cz
--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]
Carry Handbag Camo Crossbody Green Concealed Collection Camouflage Rhinestone Purse Buckle Western HW qEp4xw0zw
--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
Carson Bag Holden Street kate Crossbody Ger new spade Bk york Pbt qpSXqnB0P
Small Dray Lucky Praline Crossbody Copper UfgTp

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