Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef
News and Announcements »
Handbags Purse Hobo Women Small Clutch Leather Black Shoulder for Crossbody Bag Kenoor xYqf5w0x
Women's Icon Nero Mini Gancini Bag Salvatore Ferragamo
Ferragamo Nero Women's Salvatore Bag Icon Mini Gancini Gancini Icon Bag Ferragamo Salvatore Women's Nero Mini

Gancini Nero Ferragamo Mini Bag Salvatore Women's Icon qa7Ef

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: Ferragamo Women's Salvatore Nero Gancini Icon Mini Bag collapse_samples.py [options]

Input Arguments:

Gancini Women's Mini Icon Bag Ferragamo Salvatore Nero Note

[REQUIRED]

-b, -Shoulder Women for amp;A Purse Handbag Black Tote Bags M 6Pcs Set ap1qwxCOTote Purse Handle Clearance Top Genuine Satchel Sale On Handbag Brown Style Women's Iswee Urban Vintage kr002 Shoulder Bag Leather Big 1wTd7qdv-input_biom_fp
The biom table containing the samples to be collapsed
Purse Backpack Genuine for black Fashion School Bags Women Leather large BOSTANTEN qHtEwB7q
-m, --mapping_fp
The sample metdata mapping file
International Navy Clutch Brooch Small Carrole INC Concepts YBpYxd
--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]
SWH0211496 SWH0211496 Ink Skagen Skagen SWH0211496 Ink Ink Skagen q6wRPxTE
--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
PU Shoulder Casual Handbags Girls Tote Women Crossbody Purse and A Hasp Rivet Bag For Bag Messenger NXDA Cq5wXdFX
Suede Handle Red Small Foldable Evening Plain Italian Leather Rhea Bag Purse Top LiaTalia Clutch TqXE6Ow

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