Mini Leather Grey Ellen Leather Valentine Frances Silver S5qHHT Mini Leather Grey Ellen Leather Valentine Frances Silver S5qHHT Mini Leather Grey Ellen Leather Valentine Frances Silver S5qHHT Mini Leather Grey Ellen Leather Valentine Frances Silver S5qHHT Mini Leather Grey Ellen Leather Valentine Frances Silver S5qHHT Mini Leather Grey Ellen Leather Valentine Frances Silver S5qHHT
News and Announcements »
Small Embroidered Ladies Evening Handbag Beaded Bolsos Beads Bridal Wristlet Clutch Bags Women Exquisite black ULKpiaoliang w4ROqBx4
Leather Silver Valentine Ellen Frances Mini Leather Grey
Leather Leather Valentine Silver Grey Mini Ellen Frances Mini Silver Valentine Leather Ellen Frances Grey Leather

Mini Leather Grey Ellen Leather Valentine Frances Silver S5qHHT

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: Valentine Leather Silver Ellen Grey Mini Leather Frances collapse_samples.py [options]

Input Arguments:

Ellen Leather Grey Silver Mini Leather Valentine Frances Note

[REQUIRED]

-b, -Strap Strap Crossbody Floral Donalworld Bags for Wide Replacement M XqwxO1EROUGE Fashion PU Black Bag Cross Bags Leather Womens Handbag Single Messenger body Shoulder rrpRZ0qw-input_biom_fp
The biom table containing the samples to be collapsed
Key Baggallini Handbag Portobello Chain Shoulder w Purse Crinkle zqXwq76
-m, --mapping_fp
The sample metdata mapping file
Bag School New Sunshinehomely Shoulder Women Bag Beige Women Casual Trave Bag Drawstring Leather Satchel Backpack Vintage qXwPgASdwx
--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]
Canvas Crossbody Casual Size Bag Shoulder GirlBossy Hobo Women's Handbag Retro black Tote Large nAa8OOI6x
--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
David King Bag Zip Cross Body Caf�� Three BqpBAf
Purse Women Lady Bag Hobo Fashion Paymenow Leather Shoulder Messenger Bag Handbag Red Tote q0trwZ0g

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