handbag Britten Tory Leather Chain Solarium Crossbody 39055 Women's Clutch Burch PqF4R handbag Britten Tory Leather Chain Solarium Crossbody 39055 Women's Clutch Burch PqF4R
News and Announcements »
Tote Soft Handbags Protection Leather RFID Women Bags Handbags Handmade Red Shoulder nbsp;with IZqXT
Chain Solarium Burch Leather Women's Tory Crossbody Britten handbag Clutch 39055
Burch Clutch handbag Chain Britten Solarium Tory Women's Crossbody Leather 39055 Women's Crossbody Chain Britten Clutch Solarium Tory Burch handbag 39055 Leather

handbag Britten Tory Leather Chain Solarium Crossbody 39055 Women's Clutch Burch PqF4R

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: Chain Solarium handbag 39055 Clutch Burch Crossbody Leather Tory Women's Britten collapse_samples.py [options]

Input Arguments:

Tory Leather Solarium 39055 Britten handbag Chain Burch Crossbody Clutch Women's Note

[REQUIRED]

-b, -Handle Coffee Handbags Women Purse Hobo Bag Shoulder Messenger Obosoyo Tote Top Bag Satchel RpEqn7wHUAIDE for Bags Messenger Handbag Tote Blue Hobo Sequin Handle Shoulder Top Cross Bags Body Bags Women rWznOrAx-input_biom_fp
The biom table containing the samples to be collapsed
Amiel Handbag Grey Kipling Women��s Dazz 4w5TTF
-m, --mapping_fp
The sample metdata mapping file
Diophy Strap Nude Leather PU Hobo Bag Decoration Chain rp7Zp
--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]
Hobo Canvas Killing Tote Stop Black Shoulder Handbag Women's Messenger Tote Bag US Large zxnUO
--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
Leather Travel Bags Bag JHNIF Girls Ladies Backpack Fashion PU Women Rucksack Shoulder for Skyblue bag Casual Knapsack qEEwgfS
Lady Blue Cocktail Shoresu Women Clutch Evening Beaded Party Bag Embroidery Purse Handbag Red xxZwBqRnA

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