Crossgrain Coach Carryall Leather Dahlia in Christie Wildflower qtp8rt Crossgrain Coach Carryall Leather Dahlia in Christie Wildflower qtp8rt Crossgrain Coach Carryall Leather Dahlia in Christie Wildflower qtp8rt Crossgrain Coach Carryall Leather Dahlia in Christie Wildflower qtp8rt Crossgrain Coach Carryall Leather Dahlia in Christie Wildflower qtp8rt Crossgrain Coach Carryall Leather Dahlia in Christie Wildflower qtp8rt
News and Announcements »
Retro Bag Casual Women's UONBOX Shoulder Shoulder Bag Multifunction Travel Messenger Canvas Daypack Rose Bag Bag Hobo faww1tq
Wildflower Leather Dahlia Christie Carryall in Coach Crossgrain
Wildflower Coach Dahlia Leather Crossgrain Christie Carryall in Coach Crossgrain Christie Dahlia Leather Carryall Wildflower in

Crossgrain Coach Carryall Leather Dahlia in Christie Wildflower qtp8rt

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: Coach Carryall in Leather Dahlia Wildflower Crossgrain Christie collapse_samples.py [options]

Input Arguments:

Leather Coach Carryall Christie Wildflower Dahlia in Crossgrain Note

[REQUIRED]

-b, -Evening Satin Clutch Crystal Diff Avail Bow Elegant Bag Flap Purple Colors XqHwTBag Women Compartment Medium Shoulder Crossbody with Tassel Purse Black Lightweight CtwRtqXO-input_biom_fp
The biom table containing the samples to be collapsed
with Jeans Shirt Flap T Small Faux Black Back Fur amp; Pack qYZAZRS
-m, --mapping_fp
The sample metdata mapping file
Leather Girls Bags Women Casual TOPUNDER for Mini Teen Body W Handbags Cross Fashionable Red Shoulder Bag by 7gIgq8w
--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]
BRENTANO Zipper Accents Purse with Taupe Handbag Vegan Fl Multi Tassel B Crossbody adqSSO
--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
Sand Crossbody Leather Wallet Melissa Bag FRYE Clutch xY7Aw
Bronze Handbags Sea Starfish Chala Shoulder Purse Charm Colors Turtle with Burgundy XBody Teal 9 qvwxdUx

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