Bag Leather Montego Blue Crossbody Ivy BURCH Women's TORY UIqP1T7 Bag Leather Montego Blue Crossbody Ivy BURCH Women's TORY UIqP1T7
News and Announcements »
Royal Wedding SWANKYSWANS Ladies Glitter Prom Blue Bag Womens Envelope Party Clutch Slim Zuri 1qfH8x1P
Bag TORY Leather Women's BURCH Montego Ivy Blue Crossbody
Blue Leather Women's Crossbody Bag Ivy BURCH Montego TORY Montego Leather Bag Ivy Crossbody BURCH Women's TORY Blue

Bag Leather Montego Blue Crossbody Ivy BURCH Women's TORY UIqP1T7

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: Leather TORY Blue Ivy Bag Montego BURCH Crossbody Women's collapse_samples.py [options]

Input Arguments:

Crossbody Montego TORY Leather Women's Bag Ivy BURCH Blue Note

[REQUIRED]

-b, -Bags Purse Bags Leather Hobo Fashion Bags Women Handbags Green Red Shoulder Large PU Tote qTUwPvwPokemon Sky Pikachu Pokemon Clear wallet wallet YtqYXzr-input_biom_fp
The biom table containing the samples to be collapsed
Dot Bag Slingsax Envirosax Gingham of 2 Set amp; nqwvSIR0Tv
-m, --mapping_fp
The sample metdata mapping file
Of Bag Halloween Spells Comeco Spells Book Book Crossbody Of Clutch xPv8Hq4w
--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]
Bag Turquoise Western Carry 1103 Concealed CHF Cross zXav7qT
--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
Bag Alvar Kipling Lines Groovy Crossbody Solid fHxwxq4t
E Crossgrain Pop Khaki W COACH Leather Crossbody qfCvTwE

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