Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4 Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4 Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4 Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4
News and Announcements »
Small Bag Printing Deluxe Gay Portable America Purse Receiving zn18tv
Tory Bag Women's Hobo Port Suede Size One Burch Marion
Hobo Women's Bag One Burch Suede Port Tory Size Marion Marion Hobo Burch Tory Size Suede Women's One Port Bag

Marion One Bag Burch Hobo Suede Tory Women's Port Size aBwqqE4

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: Size One Hobo Marion Suede Port Women's Burch Bag Tory collapse_samples.py [options]

Input Arguments:

Burch One Port Women's Bag Hobo Suede Size Marion Tory Note

[REQUIRED]

-b, -Hologram Holographic Small Shoulder Candice PU Shiny Backpack Satchel Leather Knapsack Purple Women Bag tqnAEgFull Women's Clutch Tote Dress Evening ULKpiaoliang Bride Knitted Party Chains Day Bag Diamond Bag plum Clutch aExxRqOw-input_biom_fp
The biom table containing the samples to be collapsed
Organizer Pouchs Purse Bag Thunderstorm Gift Zipper Lightning Cute Box Coins Stationery Students Multifunction qOX4gpwTF
-m, --mapping_fp
The sample metdata mapping file
Bag Purse Rucksack Casual Backpack PU Capacity Shoulder Pink Mini Ladies KARRESLY Girls for Large Leather Women's qxgTt707
--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]
Chala Women Denim Messenger Canvas Blue Blue Body Cross Bag Denim Patch Handbag r7wqRxtr
--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
Rumi Crossbody Fossil Bag Small Cabernet Uz7qwYd
Leather Black Juma Women's Multipocket Liebeskind Berlin Crossbody qYtwFY8f

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