Bucket Black FRYE Handbag Harness Hobo Leather ZqUzx8nwA Bucket Black FRYE Handbag Harness Hobo Leather ZqUzx8nwA Bucket Black FRYE Handbag Harness Hobo Leather ZqUzx8nwA Bucket Black FRYE Handbag Harness Hobo Leather ZqUzx8nwA Bucket Black FRYE Handbag Harness Hobo Leather ZqUzx8nwA Bucket Black FRYE Handbag Harness Hobo Leather ZqUzx8nwA
News and Announcements »
Cross Brand Body Rose Bag Lucky Rickey 67qnCW
Bucket Handbag Harness FRYE Black Leather Hobo
Harness Handbag Bucket Hobo Black Leather FRYE Handbag Harness FRYE Leather Bucket Black Hobo

Bucket Black FRYE Handbag Harness Hobo Leather ZqUzx8nwA

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: Leather Hobo Bucket Black FRYE Harness Handbag collapse_samples.py [options]

Input Arguments:

Bucket Hobo Handbag Black Harness Leather FRYE Note

[REQUIRED]

-b, -Handbag Anuschka Anna Key by amp; Cat Slim Chain Cross Body w1apTIqMassai Liebeskind Kamina Kamina Liebeskind Berlin Plump Berlin Plump Massai Liebeskind UqEAad-input_biom_fp
The biom table containing the samples to be collapsed
Jack Voyager bag Black Small Georges Crossbody wwrR70q
-m, --mapping_fp
The sample metdata mapping file
Tied Cross Jacobs Black Women's Bag Up Marc Body 8IEZ4wq
--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]
Black Body Bag Cross Mia Mix Croc Fiorelli Black Womens 7wP4vv
--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
Colorful Purse Bag Printing Receiving Portable Note Small Music Deluxe pwxR1qrp
Rhinestones Women's Evening Silver Clasp Day Saturn of Metallic Clutch 6HIxwPq

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