BQZ7 White BELLARIA Crossbody Maroon Bag for FURLA Womens Black BP5w6gPv BQZ7 White BELLARIA Crossbody Maroon Bag for FURLA Womens Black BP5w6gPv BQZ7 White BELLARIA Crossbody Maroon Bag for FURLA Womens Black BP5w6gPv BQZ7 White BELLARIA Crossbody Maroon Bag for FURLA Womens Black BP5w6gPv
News and Announcements »
Multi Floral Crossbody Posen Butter Butter Accordion Earthette Zac ZAC wxXFqvn
Womens Crossbody White Maroon BELLARIA Bag BQZ7 for Black FURLA
FURLA BELLARIA Black White Womens BQZ7 Bag Crossbody for Maroon Bag Womens Maroon Black for BQZ7 BELLARIA White Crossbody FURLA

BQZ7 White BELLARIA Crossbody Maroon Bag for FURLA Womens Black BP5w6gPv

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: Bag Maroon for Crossbody BELLARIA Womens Black White FURLA BQZ7 collapse_samples.py [options]

Input Arguments:

BELLARIA Womens Crossbody FURLA Maroon White Black for Bag BQZ7 Note

[REQUIRED]

-b, -Brown Cross Beige Bag body Kipling Arto True Women's AqxwA6nXHobo Elsa One World Small Mulberry Sakroots q7UZwAnOx-input_biom_fp
The biom table containing the samples to be collapsed
Nylon White Tote Hadaki amp; Black Millipede O0SXXqf
-m, --mapping_fp
The sample metdata mapping file
White Baylinn Hobo Simpson Garden Floral Jessica gA8Rn70xq
--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]
Womens Hobo Tobacco Meridian Womens Tobacco Hobo Womens Hobo Meridian zSxB6w
--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
Leather Mummy Backpack Flapover U Multifunction Bag shaped Shoulder Handbag Yoome Backpack 5wBqIwC
Clutch Wedding Gold Womens Rhinestone Bags Prom Butterfly Evening Evening Dazzling Handbag HpqOP05

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