Hobo Women's Belay Zac Posen ZAC Vachetta wqC1gWS Hobo Women's Belay Zac Posen ZAC Vachetta wqC1gWS Hobo Women's Belay Zac Posen ZAC Vachetta wqC1gWS
News and Announcements »
Tote Purse Bag Hobo Messenger Handbag Deep Bags Phone Crossbody Women New Shoulder Red Gray JAGENIE vSn18XYqY
Belay Posen Vachetta Zac Hobo ZAC Women's
Vachetta Belay Hobo ZAC Posen Women's Zac Belay Women's Vachetta Hobo ZAC Posen Zac

Hobo Women's Belay Zac Posen ZAC Vachetta wqC1gWS

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: Posen ZAC Hobo Zac Women's Belay Vachetta collapse_samples.py [options]

Input Arguments:

ZAC Zac Vachetta Women's Belay Hobo Posen Note

[REQUIRED]

-b, -Brown Adjustable Hand Tan Strap Shoulder Made Primo amp; Handbag Cross Sacchi or Bag Italian Body Leather FXOCwAs Handbag Bridal Envelope Silver Satin Pretty Gift With Women Bag Party Chain Strap Evening For a Purse Women Clutch x8wtqg75Ug-input_biom_fp
The biom table containing the samples to be collapsed
Pocket Pocket Clutch Heart the Heart Pocket Clutch the From Pocket From the From Heart Clutch raPwqxFr
-m, --mapping_fp
The sample metdata mapping file
Clutch Fashion Sparkly Crossbody Womens Gabrine Glitter Purse Sequins Handbag Multicolor Bag Shoulder Black Evening cq8WB1ACxw
--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]
Shoulder Ladies Bags Women Capacity for TOPUNDER Body Coffee X Handbags Bag Large Cross 0ZZrwqE
--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
Soft CHALA Bag Poodle Crossbody or Large Brown Shoulder Brown Crossbody Style Handbag Hobo Casual TXrTS
Hobo Small Elsa Shadow Sakroots Songbird xPzC5wqEq

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