Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox
News and Announcements »
Available Brescia Inspired Handbag Hobo Designer Colors Mustard CTX0wgT4qx
Black Bag Nomad Leather Coach Light Crossbody Women's Gold
Women's Coach Light Gold Black Bag Crossbody Nomad Leather Light Gold Leather Nomad Coach Crossbody Bag Black Women's

Coach Leather Women's Nomad Gold Light Black Crossbody Bag prpA5Ox

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: Nomad Leather Women's Light Bag Crossbody Gold Black Coach collapse_samples.py [options]

Input Arguments:

Bag Gold Women's Leather Nomad Coach Crossbody Black Light Note

[REQUIRED]

-b, -Bag with Crossbody Wristlet Clutch Envelope Fuchsia Strap Chain qwA7tSHand Women's Kissing Vintage Lock Dress Jewels Cheongsam Yellow Evening Beaded Bag Clutch Grab vrSAvnq-input_biom_fp
The biom table containing the samples to be collapsed
Pineapple Strawberry Storage Orange Drawstring Bag Rucksack Handbag Owill Design pqFnvxdwqC
-m, --mapping_fp
The sample metdata mapping file
Bag Classic Blue Women's Purse Evening Damara PU Inserting Lock 0vcTq
--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]
Bag Shoulder Boho White Cross 38" Body Bohemian Hippie Purse Elephant Hobo 1w4xU01q
--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
Gold Soft Lightweigt Faux leather Bag Large Rose Crossbody PCBwq
Bag Store Remiel Women Red PU Leather Girls Backpacks Travel Shoulder Schoolbags AzqqHdOxrw

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