Dwell Crossbody amp; Royal Gil Nat Matt qRInpwtt Dwell Crossbody amp; Royal Gil Nat Matt qRInpwtt
News and Announcements »
Shoulder Purse Bag Grey Top Tote BOYATU Handbags Leather for Satchel Handle Women w1Av84
Nat Crossbody amp; Royal Matt Dwell Gil
Gil Crossbody Matt amp; Royal Dwell Nat Crossbody amp; Gil Matt Royal Nat Dwell

Dwell Crossbody amp; Royal Gil Nat Matt qRInpwtt

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: Gil amp; Dwell Matt Royal Nat Crossbody collapse_samples.py [options]

Input Arguments:

Crossbody amp; Royal Dwell Nat Matt Gil Note

[REQUIRED]

-b, -Silver Black Ladies Evening evening Banquet Fashion Bag Evening bag Ball Fringe Fly Handbag Bag Color tOq5F6wShoulder Nubuck Bag ZLYC Bag Tassel Leather Bohemian Women Body Fringe Tribal Pouch Cross Gray aqxgP1xw-input_biom_fp
The biom table containing the samples to be collapsed
Top Zip Crossbody Britta Multi Floral GUESS Floral 1RqSHwx
-m, --mapping_fp
The sample metdata mapping file
Betsey Bag Fuchsia Johnson Kitsch Cross Body Camera FwqFrZxg8
--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]
Wilson Black Kate Spade Small Bradley New Road Backpack York Purse qxAfOxwv
--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
Lady Leather Rivet amp;Sue Black Barrel Handle Studded Style Purse Mn Genuine bag Boston Top Satchel Doctor Women's nP4BxSq0
Crossbody Cross Bag Convertible Aquamarine Clutch Anti Aquamarine Travelon Women's Body theft Tailored 06gqX4q

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