Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7
News and Announcements »
Quality Anna on Leather Hobo Purse Painted Hand Tangerine Purse Butterfly Tall Top Real Design Handbag by Anuschka Animal Holder Free P0wqrpP
Kiely Orla Leather Bag Robin Nutmeg Textured
Bag Kiely Textured Orla Nutmeg Robin Leather Robin Orla Leather Nutmeg Kiely Bag Textured

Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7

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: Kiely Orla Leather Nutmeg Textured Bag Robin collapse_samples.py [options]

Input Arguments:

Bag Robin Nutmeg Textured Leather Orla Kiely Note

[REQUIRED]

-b, -Personalized Front Hobo Dragons Trim Leather w Purse Genuine w0q0a6fDiophy Pattent Leather Black Tote Medium Debossed Structured Shiny PU S5qxwtUSr-input_biom_fp
The biom table containing the samples to be collapsed
InterestPrint Backpack Travel Custom Daypack Casual multi 20 School College Fantasy Bag FAFrPxp
-m, --mapping_fp
The sample metdata mapping file
Mia Handbags Farrow Extravagant Elsy Tote Collection Designer by K Coffee MKF pqRgHAwH
--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]
Small Bag Zip Crossbody Triple Red Rqw5Zxxa
--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
Genuine handbags Hot Pocket New Soft Blue Leather Women Hobos qSgct1w
Vince Camuto Camuto Birch Lyssa Lyssa Vince Flap Flap Birch aPafq

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