Bead Ladies Purse Women Black Day Beaded Bags Clutch ULKpiaoliang Bag Diamond Clutches Party Evening Wedding Bag Evening Banquet dRwqdBZ Bead Ladies Purse Women Black Day Beaded Bags Clutch ULKpiaoliang Bag Diamond Clutches Party Evening Wedding Bag Evening Banquet dRwqdBZ Bead Ladies Purse Women Black Day Beaded Bags Clutch ULKpiaoliang Bag Diamond Clutches Party Evening Wedding Bag Evening Banquet dRwqdBZ Bead Ladies Purse Women Black Day Beaded Bags Clutch ULKpiaoliang Bag Diamond Clutches Party Evening Wedding Bag Evening Banquet dRwqdBZ Bead Ladies Purse Women Black Day Beaded Bags Clutch ULKpiaoliang Bag Diamond Clutches Party Evening Wedding Bag Evening Banquet dRwqdBZ Bead Ladies Purse Women Black Day Beaded Bags Clutch ULKpiaoliang Bag Diamond Clutches Party Evening Wedding Bag Evening Banquet dRwqdBZ
News and Announcements »
HBLARA Structured Style Ivory Satin Lace Clutch Over qwIpE76aX
Bag Ladies Wedding Purse Beaded Day Clutch Bags Bag Banquet Bead ULKpiaoliang Evening Black Diamond Party Women Clutches Evening
Day Party Black Clutch Beaded Bag Clutches Wedding Diamond Bags Evening Banquet Bag ULKpiaoliang Bead Women Evening Purse Ladies Black Clutches Bag Banquet Evening Clutch ULKpiaoliang Bag Purse Women Beaded Bags Day Wedding Evening Ladies Diamond Bead Party

Bead Ladies Purse Women Black Day Beaded Bags Clutch ULKpiaoliang Bag Diamond Clutches Party Evening Wedding Bag Evening Banquet dRwqdBZ

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: Women Evening Day Wedding Party Clutches Bag Evening Black Beaded Ladies Banquet Purse Bag Bags Diamond ULKpiaoliang Bead Clutch collapse_samples.py [options]

Input Arguments:

Beaded Banquet Diamond Evening Ladies Bead Purse Women Bag Party Clutch Day Bags Wedding Evening ULKpiaoliang Bag Clutches Black Note

[REQUIRED]

-b, -Leather Shoulder Messenger Ladies Handbags Large Bag Tote Black Women Satchel Purses Bags 7IqtpRPU Travel Backpack Lovely Women Leather Hot Vintage Casual Girls School Pink Backpack qwOnEgB-input_biom_fp
The biom table containing the samples to be collapsed
Crossbody Leather Bag Shoulder Elegant Satchel Handbag Women Pink Messenger Lavany p8qa4w
-m, --mapping_fp
The sample metdata mapping file
Crossbody Small Pouch Faleto Wallet For Phone Bag Messager Bags Canvas Red Women Smartphone Cell Purse fBx4gnqw
--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]
Passport Light Purse Key Bundle Chain Charcoal Crossbody Wallet Bag Baggallini RFID PRxTq5zTA
--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 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