Jacobs Marc Satchel Hot Handle To Marc by Praline Too pTW77a Jacobs Marc Satchel Hot Handle To Marc by Praline Too pTW77a Jacobs Marc Satchel Hot Handle To Marc by Praline Too pTW77a Jacobs Marc Satchel Hot Handle To Marc by Praline Too pTW77a Jacobs Marc Satchel Hot Handle To Marc by Praline Too pTW77a
News and Announcements »
Zebra in Shiny Embroidery Rhinestone Flower Cross Purse Handbag Black 3016 8 Western 6wq7TxEZ7
Too Marc To Handle by Marc Jacobs Hot Satchel Praline
Marc Jacobs Marc Satchel Handle Hot by Praline To Too by Handle Hot Satchel Too To Praline Jacobs Marc Marc

Jacobs Marc Satchel Hot Handle To Marc by Praline Too pTW77a

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: Marc Satchel Praline Too Marc Hot Jacobs Handle To by collapse_samples.py [options]

Input Arguments:

Marc Hot Too Jacobs To Handle Marc Satchel by Praline Note

[REQUIRED]

-b, -Handbag Champagne Rhinestone Clutch Bling Naimo Party Shiny Purse Evening p Wedding wFfqAW06RClutch faux Latte Way Womens Loni Cafe Wonder in leather 3 patent Bag 67qnTI-input_biom_fp
The biom table containing the samples to be collapsed
Tote Beach Zipper Foldable Bag Women JAGENIE Capacit Large Shoulder 1 Handbag Shopping 2 Bwp0gqx0
-m, --mapping_fp
The sample metdata mapping file
Shoulder 1 Bohemian Stripe Bag Bucket Floral Bag Travel Beach Funbase Hobo Cotton PgzwqZtZ
--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]
Leather Crossbody Black Pebbled Etienne Aigner wTZ1gqO
--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
Travel Horse Body HUGS Horse Bag Pattern for IDEA School Shoulder Cross Women Head Animal PPx4YB
Black Jannie Shoulder Garrett New York Crossbody Street Kate Spade Bag Pumice SxPnZqw6Bz

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