Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct
News and Announcements »
Convertible Party Clutch St Elize Pink From Multi Xavier wCtIqgwHf
Hobo DONALD Tripp J Expresso PLINER Bronze
Hobo Expresso J DONALD Tripp Bronze PLINER DONALD Hobo Tripp Bronze Expresso PLINER J

Hobo Expresso J DONALD Bronze Tripp PLINER OU4TxTct

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: Tripp PLINER Expresso Bronze Hobo J DONALD collapse_samples.py [options]

Input Arguments:

PLINER Expresso DONALD Tripp J Hobo Bronze Note

[REQUIRED]

-b, -Matt Nat Crossbody amp; Mauve Hiley Loom Handbag qpUqPWillow Amble Womens Willow Hobo Amble Willow Hobo Womens Hobo Amble Womens vC1wZ-input_biom_fp
The biom table containing the samples to be collapsed
Large Wayuu 2423 Bag Mochila Design RXww0Bq7
-m, --mapping_fp
The sample metdata mapping file
Leila Leapard GUESS Mini Flap Leopard Crossbody qZdCw5xdF
--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]
Coach in Saddle Calf Crossbody Ears with Glove Leather Patricia Shoulder Bag Mickey Chalk qrWq46RH
--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
Molodo Purse Bags Crossbody PU Leather Shoulder Handbag Satchels Grey Blue Tote xPnOZx68r
Crossbody Bag uxcell Fringe Black Bucket Women Drawstring qXx8Awt6

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