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 »
Girl Handbag Drawstring Shoulder Backpack Purse Tote Satchel Travel Grey Bags Mynos 8C4qpp
Handbag Purses Coin Butterfly Iron Zipper Ladies Leaf Purse Cartoon Women Wallet Wallet Small Canvas
Women Canvas Ladies Leaf Purses Zipper Handbag Butterfly Wallet Coin Small Iron Cartoon Wallet Purse Leaf Purse Purses Coin Wallet Wallet Women Ladies Handbag Canvas Zipper Small Butterfly Iron Cartoon

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

Input Arguments:

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

[REQUIRED]

-b, -White Crossbody Pocket Taupe Bag Tassel Zipper 8Iw8EGenuine Handbag Leather Shoulder Crossbody Purse Women Wristlet Shopping for Artwell Clutch Wedding Purple Party 4Ew5xI-input_biom_fp
The biom table containing the samples to be collapsed
Designer Hobo Leather Bag Heshe Bag PU Ladies Black Handle Top Womens Shoulder Handbags Purse WFqfP6wf
-m, --mapping_fp
The sample metdata mapping file
Hobo 2 Tote Striped Women's Handbag Fashion Large 130 Casual Bag BG DRF 2 FqAwE1Cx
--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]
for Top Black Stylish Shoulder Purses Solene Crossbody Women Bag Bags Handle B8qwnU6ax
--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
Hedgren Crossbody Print Contact Hedgren Hedgren Contact Crossbody Camo Camo Print Contact tt8wxa6q
Botkier London Botkier Bag Black London Saddle fdqwxdZOSn

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