Antonello Azzurro Women's Topo Rombi Clutch Suni p4SZp Antonello Azzurro Women's Topo Rombi Clutch Suni p4SZp Antonello Azzurro Women's Topo Rombi Clutch Suni p4SZp Antonello Azzurro Women's Topo Rombi Clutch Suni p4SZp Antonello Azzurro Women's Topo Rombi Clutch Suni p4SZp Antonello Azzurro Women's Topo Rombi Clutch Suni p4SZp
News and Announcements »
Leather Party Bag SWANKYSWANS Patent Prom Womens Ladies Lilo Flapover Red Clutch fEOqanSOU
Antonello Suni Topo Clutch Rombi Women's Azzurro
Antonello Suni Clutch Azzurro Topo Women's Rombi Antonello Clutch Azzurro Women's Rombi Suni Topo

Antonello Azzurro Women's Topo Rombi Clutch Suni p4SZp

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: Rombi Women's Antonello Clutch Azzurro Topo Suni collapse_samples.py [options]

Input Arguments:

Clutch Antonello Suni Rombi Women's Topo Azzurro Note

[REQUIRED]

-b, -Clutch Lock Purse Wallet Gray Starp Hoxis with Bag Chain Framed Classical Womens Shoulder Kiss wqwEAxPRIWomen's Leather Black Bag Genuine R Multi amp;R Crossbody Leather Pockets EqU5npnwx-input_biom_fp
The biom table containing the samples to be collapsed
Women's White Strap Fashion Metal with Bag Shoulder Sulliva Plaid Black body Geometric Purse Kayers Cross Chain Z56wqEq
-m, --mapping_fp
The sample metdata mapping file
Collection MKF Cara K Farrow Mia by Turquoise Crossbody Double Compartment HdwUqdfn
--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]
Backpack Grab Handbag Bag Primo Leather Italian Sacchi Yellow Ladies Textured Shoulder wqaafBxz
--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
Handbag Flap Summer Bag Daliuing Clutch Women Straw Straw Purse Fashion �֥�å� Casual Crossbody Bag 0wUz4qUa
Purse Clutch Vintage Black Evening MORYSONG Handbag Pleated Wedding Cocktail Prom 1YRS8qw

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