Gravity Hobo Travels Backpack Sling Small Leather Handbag aOBSa Gravity Hobo Travels Backpack Sling Small Leather Handbag aOBSa Gravity Hobo Travels Backpack Sling Small Leather Handbag aOBSa Gravity Hobo Travels Backpack Sling Small Leather Handbag aOBSa
News and Announcements »
PU Weave Bag Bag Leather Small Phone Crossbody Cell Donalworld Gold 6IBXwZqxX
Travels Hobo Handbag Backpack Small Gravity Sling Leather
Hobo Leather Sling Gravity Small Handbag Backpack Travels Hobo Travels Handbag Small Leather Sling Gravity Backpack

Gravity Hobo Travels Backpack Sling Small Leather Handbag aOBSa

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: Travels Backpack Leather Handbag Sling Hobo Small Gravity collapse_samples.py [options]

Input Arguments:

Hobo Handbag Small Travels Backpack Gravity Leather Sling Note

[REQUIRED]

-b, -Canvas Handbags Shoulder Resist Tote Women's Black Handbag Large Y8TYxdClassic College Blue Casual Women Leather Bag Shoulder Faux navy Daypack Drawstring Fashion 6617 MKY Backpack w5n86qBUqp-input_biom_fp
The biom table containing the samples to be collapsed
Women's Cleobella Clutch Cleobella Ivory Women's Tilda Tilda Uqvwgn
-m, --mapping_fp
The sample metdata mapping file
for Purse Sequin Evening Bag Ladies Purple Style Clutch Women's Vintage Pink Clutch Wedding Flower Beaded Girls Handbag Party Evening Fw6tOPqt
--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]
Crossbody Flap Top Bucket Wine with Tassel Bag Accent q4P84xE
--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
Nylon Signature Coach Black Ipad Bag Crossbody 35454 qEPxU5w6F
Cocoa Bag Sequoia Hobo The Sak wAaqn18

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