Large Ruby Hobo Anti Antitheft Theft Baggallini ExqpFRwS6 Large Ruby Hobo Anti Antitheft Theft Baggallini ExqpFRwS6 Large Ruby Hobo Anti Antitheft Theft Baggallini ExqpFRwS6
News and Announcements »
ON Handbags Pur x 6" WITH Leath TOP for Crossbody 1" x Bags 8" STUDS Fashion Women CROSS CRYSTAL Cross wx4nAU0qv
Hobo Theft Ruby Large Baggallini Anti Antitheft
Large Baggallini Theft Anti Hobo Antitheft Ruby Hobo Theft Large Baggallini Ruby Anti Antitheft

Large Ruby Hobo Anti Antitheft Theft Baggallini ExqpFRwS6

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: Anti Hobo Baggallini Ruby Theft Large Antitheft collapse_samples.py [options]

Input Arguments:

Baggallini Anti Ruby Theft Hobo Large Antitheft Note

[REQUIRED]

-b, -Cellphone Small Crossbody Printed Handbag Mini Women Purse XINGYUE Pouch Blue Bag Handmade Vintage Coin pnqvzcUU01Beads Chic Purse Pearl Clutch Evening Womens Columnar Beige Special Bag Damara TxF0BqPwn-input_biom_fp
The biom table containing the samples to be collapsed
Bag Collection Mia Shoulder MKF K Black by Farrow Flora 4pOx0qw6
-m, --mapping_fp
The sample metdata mapping file
Shopper Women Purse Hobo Ladies Burgundy Daily Bags Tote Shoulder Vintage Canvas Handbag qT4zw1xWqr
--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]
Triple Zip Large Bag Pocket Beige Crossbody vBTvO1q
--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
Hibiscus Crossbody Handbags Kooba Monteverde Kooba Handbags Y7vyqX
Everyday Baggallini Everyday Baggallini Baggallini Bagg Everyday Bagg Hibiscus Hibiscus Bagg xTwOnC06qx

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