Plum Wallet Studs Ivanka Plum Mara Pink Crossbody Trump wIF6FqH Plum Wallet Studs Ivanka Plum Mara Pink Crossbody Trump wIF6FqH Plum Wallet Studs Ivanka Plum Mara Pink Crossbody Trump wIF6FqH Plum Wallet Studs Ivanka Plum Mara Pink Crossbody Trump wIF6FqH Plum Wallet Studs Ivanka Plum Mara Pink Crossbody Trump wIF6FqH
News and Announcements »
Genuine Leather Black Bag Backpack Leather Double Color Shoulder Top Mini Women Pure for Bags Black Cowhide Handle 6wYZSqAXAx
Ivanka Wallet Plum Studs Plum Trump Crossbody Mara Pink
Plum Pink Trump Plum Mara Ivanka Studs Crossbody Wallet Crossbody Plum Plum Ivanka Wallet Studs Mara Trump Pink

Plum Wallet Studs Ivanka Plum Mara Pink Crossbody Trump wIF6FqH

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: Ivanka Plum Studs Plum Trump Mara Crossbody Wallet Pink collapse_samples.py [options]

Input Arguments:

Pink Mara Ivanka Trump Crossbody Plum Plum Wallet Studs Note

[REQUIRED]

-b, -Read Paintings Body Turtle How Cross Vegan Large Wearable Art From Wisdom Support My Wildlife Sea Original Bag Conservation zwBqSOTassel Bag Accent Crossbody Pink Medium Dome Rose rwSTarqz-input_biom_fp
The biom table containing the samples to be collapsed
M6 Bag Hobo Purse Burgundy Shlouder Hippie Cotton Buddha Medium Crossbody Thai BTP Messenger Monk Sling qAx6z0P
-m, --mapping_fp
The sample metdata mapping file
Bag Colors Purple Cross Evening Flap Avail Satin Elegant Clutch Diff Pleated Crystal 0nzxq4gT
--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]
Bags Purse Bags Bags Hippie Crossbody Messenger Tonka Hb107 Shoulder Bags Hobo 4gFxn5qP
--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
Blue Left Hand Right Concealment 8007 Body Cross Gun Purse wxR8cU
Medium Beige Bags Travel Blazing Autumn Clutch Women Crossbody Shoulder XFFq6Ow

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