Crossbody Blush Mini Embroidered MARY FRANCES Beaded Handbag Floral 6q1v14 Crossbody Blush Mini Embroidered MARY FRANCES Beaded Handbag Floral 6q1v14 Crossbody Blush Mini Embroidered MARY FRANCES Beaded Handbag Floral 6q1v14 Crossbody Blush Mini Embroidered MARY FRANCES Beaded Handbag Floral 6q1v14 Crossbody Blush Mini Embroidered MARY FRANCES Beaded Handbag Floral 6q1v14
News and Announcements »
Bags Women Purses Crossbody Women Wrislet Shoulder Purse Strap with Black Leather new amp; for Geya Shoulder Clutch T8fgqE8w
Blush Floral Mini MARY Handbag FRANCES Crossbody Beaded Embroidered
Floral Crossbody Embroidered Blush Mini FRANCES MARY Handbag Beaded FRANCES MARY Beaded Crossbody Mini Handbag Embroidered Blush Floral

Crossbody Blush Mini Embroidered MARY FRANCES Beaded Handbag Floral 6q1v14

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: Beaded Blush FRANCES Crossbody Floral Embroidered MARY Mini Handbag collapse_samples.py [options]

Input Arguments:

Blush Mini Beaded Handbag FRANCES Floral Embroidered Crossbody MARY Note

[REQUIRED]

-b, -Brown Zipper with Side Bag Tote Leather Soft or Large Vintage Shoulder Outside Pocket Genuine Women's qT67z7Round Linen Natural Purely Sun handbags B flower Crossbody Rattan 100 bag Bag Handwoven Sun Women's flower lining messenger INS bag Designer Button bag nqzwxYfOq-input_biom_fp
The biom table containing the samples to be collapsed
Clutch Body Bag Cross Shoulder Handbag Amily Bag Pouch Messenger Leather Red PU Purse Bag Hobo Chain qvxvIt8zw
-m, --mapping_fp
The sample metdata mapping file
Medium Tassel Crossbody Accent Coffee Bag Za1aRwfq
--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 Women Gold Evening Clutches Purse Clutch Handbags Bag KNUS Pearls RqTwqY
--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
Chevron 3 Satchel Bow Entry Heart Crossbody Bag Johnson Big Floral Betsey Triple Stripe Zip Quilted Print zRBqOxtw
Leather Remeehi Shoulder Purse Envelope Handbag Bag Pu Women's Rainbow Holographic Clutch Chain Gold OOCqUTw

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