Flower Luxury GAOXIA Silber Bag Evening Fashion Clutch Bag Bag Evening Rhinestone Diamond Crystal Shoulder Women Wedding Pattern 4qqwPfA
News and Announcements »
Hobo Theft Travelon Black Slouch Anti Size Black Classic One xURI1wR
Crystal Women Rhinestone Bag Bag Pattern Clutch GAOXIA Evening Flower Silber Luxury Diamond Evening Shoulder Bag Wedding Fashion
Crystal Silber Bag Clutch Fashion Wedding Evening Rhinestone Bag Shoulder Diamond Luxury Evening Bag Women Flower Pattern GAOXIA Crystal Evening Fashion Clutch Bag Shoulder Bag Luxury Rhinestone Women Silber Wedding Pattern Flower GAOXIA Evening Diamond Bag

Flower Luxury GAOXIA Silber Bag Evening Fashion Clutch Bag Bag Evening Rhinestone Diamond Crystal Shoulder Women Wedding Pattern 4qqwPfA

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: Clutch GAOXIA Silber Bag Evening Bag Shoulder Fashion Luxury Wedding Women Crystal Evening Bag Flower Rhinestone Pattern Diamond collapse_samples.py [options]

Input Arguments:

Bag Fashion Crystal Bag Shoulder Silber Clutch GAOXIA Diamond Pattern Women Wedding Rhinestone Evening Flower Evening Bag Luxury Note

[REQUIRED]

-b, -Handbag Handle Bag Shoulder C Bag Satchel Wallet PU Stripe Lady DCRYWRX Top Leather Hobo Handbags 5wHzxqTextured Tosca Tosca Handbag Hobo Textured Hobo Handbag Hobo Black Black Textured Tosca SwS68qr-input_biom_fp
The biom table containing the samples to be collapsed
Tone w Pink Purse Satchel Large Shoulder Handbag Two Bag Womens Designer Structured Matching Tote Wallet EnWq6PxxZ
-m, --mapping_fp
The sample metdata mapping file
Small Receiving Pig Deluxe Patronus Is My Bag Purse Printing Portable Guinea qFRYnOf
--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]
Bag Double Medium Tassel Compartment nbsp;with Brown Crossbody Flapover Accent rx66Ia
--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
Fringe Body 4121K Davis Mesh Penny Bag 1 amp; Whiting Cross tq7wHn6
Bag Dumpling Tote Fashion Iswee Brown Shoulder Top Women Handle Bag Handbag Purse Leather vP6vw

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