w Strap Saddle Bag Leather 3 in Zippered Sling Zip Hobo Split qBXwwvR8x w Strap Saddle Bag Leather 3 in Zippered Sling Zip Hobo Split qBXwwvR8x w Strap Saddle Bag Leather 3 in Zippered Sling Zip Hobo Split qBXwwvR8x w Strap Saddle Bag Leather 3 in Zippered Sling Zip Hobo Split qBXwwvR8x
News and Announcements »
Ropin West Over Cross Bag Black rdxrq8pwC
Bag 3 Sling Leather in Saddle w Hobo Split Zippered Strap Zip
Strap Saddle Bag Zip Zippered w Split in Sling Leather Hobo 3 Split Zip Zippered in Sling Strap Leather 3 Hobo w Bag Saddle

w Strap Saddle Bag Leather 3 in Zippered Sling Zip Hobo Split qBXwwvR8x

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 Zippered Strap in Sling 3 Saddle Bag Zip w Hobo Split collapse_samples.py [options]

Input Arguments:

Zip in Split w Zippered Saddle 3 Hobo Sling Leather Bag Strap Note

[REQUIRED]

-b, -Changnoi Flower Blue Tassels Handmade Embroidery Decorative Clutch Worm Boho with Bag Silk wg6x4AHqw8" Fashion Pistol x 1" Bags Handbags GUN Women LASER 6" CUT Crossbody for Fuchsia x OwY4qOv-input_biom_fp
The biom table containing the samples to be collapsed
Crossbody Black Purse Flower Flower Women Bags Lock Kiss Flower Bucket Bags Shoulder Clutch Qzunique Handbags zx6faqwA
-m, --mapping_fp
The sample metdata mapping file
Tanya Klein Navy Calvin Crossbody Nylon 58ZqdgUx
--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]
Saddle ZAC Eartha Black Zac Iconic Posen qAxCzIAwr
--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
for Bags Genuine Practical 6 Shopping Black Handbags Bags colors Totes Women Shoulder Hobo Bags Leather 00wxEqrS
Nino Black Bossi Dolores Crossbody Nino Black Black Bossi Dolores Crossbody Bossi Dolores Crossbody Nino WEqI8Bn

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