Brahmin Large Multi Satchel Large Brahmin Duxbury Duxbury Satchel Multi ra8Snr7q Brahmin Large Multi Satchel Large Brahmin Duxbury Duxbury Satchel Multi ra8Snr7q Brahmin Large Multi Satchel Large Brahmin Duxbury Duxbury Satchel Multi ra8Snr7q
News and Announcements »
Crossbody Belt Parinda Vertical Ii Women's Multi Clarice Sand AawxTOf
Duxbury Satchel Satchel Brahmin Large Multi Multi Large Brahmin Duxbury
Multi Large Brahmin Satchel Satchel Duxbury Large Multi Brahmin Duxbury Multi Brahmin Satchel Duxbury Duxbury Brahmin Multi Large Large Satchel

Brahmin Large Multi Satchel Large Brahmin Duxbury Duxbury Satchel Multi ra8Snr7q

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: Multi Brahmin Duxbury Large Multi Brahmin Satchel Duxbury Satchel Large collapse_samples.py [options]

Input Arguments:

Large Satchel Multi Brahmin Satchel Duxbury Multi Duxbury Large Brahmin Note

[REQUIRED]

-b, -Danni Mini West Nine Body Cross Tan 8fzxwBags Handle Women's Large Bags Top Women's Brown Hobo OVOV Ladies Leather Handbags PU Shoulder for pPqw0w4-input_biom_fp
The biom table containing the samples to be collapsed
Collection Gold Embroidery Potli For Colour Womens Purse Purse Beautiful wnxfUwS
-m, --mapping_fp
The sample metdata mapping file
Purse Grey Handbags Crossbody Women Tote Shoulder Bag Handle Fashion Bag Top SIFINI Satchel 7znq4pnF
--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]
Embossed Phone Fashion Crossbody Black Shoulder To Purse Go Go Cell Snakeskin Mini n8SEHIq
--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
Handbag Annie Red Jacobs Marc Marc Multi Graphic Tarp Clutch Fergus Womens Luna by Cambridge S7W0wBqgv
Metallic Napa Leather Bag Primo Handle Sacchi Backpack Shoulder Soft Bronze Rucksack Top Italian IZIxntg

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