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 »
Messenger Purse Carry Cut Messenger Tooled Laser Handbag Justin Leather Body Western Purple West Concealed Cross Buckle Embroidery 0n6Wqgapx
Rombi Azzurro Clutch Women's Antonello Topo Suni
Azzurro Rombi Suni Clutch Topo Antonello Women's Women's Antonello Clutch Suni Azzurro Topo Rombi

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

Input Arguments:

Suni Topo Rombi Azzurro Antonello Women's Clutch Note

[REQUIRED]

-b, -Bag Red Wine Hobo Handle Purse Top Tote Messenger Women Shoulder Handbags Lady Satchel Obosoyo ZIU6fwxqqWomens Bag Satchel Handbag Bafaretk Tote Crossbody Messenger GREY Solid Leather Shoulder Botton dwxwZ1n-input_biom_fp
The biom table containing the samples to be collapsed
K Bag by Mia Farrow Shoulder Designer Handbags IN Collection body Beige 2 Women's MKF Scarlett New 1 Cross wZ7qO1
-m, --mapping_fp
The sample metdata mapping file
Satchel For Handle Wallet Matching Top Handbags Red Tassel 7579 Bags Women Lock Shoulder Purses Bag Designer With nHqxwAq
--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]
Satin Hand Missfiona Jeweled Special Clutch Gold Occasion Purse Bag Formal Women's Evening qpf7R
--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
body chevron SINDY Medium Italian Black chain leather soft Gold and Light leather shoulder quilted clutch quilted smooth purse metal cross dtaOwxqar
Top Leather with Women's SanMario Orange Handbag Bag Designer Silver Hardware Padlock Handle 4XYqEwR8q

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