Purse Valentino Italian Designer Quilted Burgundy Orlandi Bag Messenger Leather wZgRxZSpn Purse Valentino Italian Designer Quilted Burgundy Orlandi Bag Messenger Leather wZgRxZSpn Purse Valentino Italian Designer Quilted Burgundy Orlandi Bag Messenger Leather wZgRxZSpn Purse Valentino Italian Designer Quilted Burgundy Orlandi Bag Messenger Leather wZgRxZSpn Purse Valentino Italian Designer Quilted Burgundy Orlandi Bag Messenger Leather wZgRxZSpn Purse Valentino Italian Designer Quilted Burgundy Orlandi Bag Messenger Leather wZgRxZSpn
News and Announcements »
Women Bags TOPUNDER Cross Colors body for Bag by Girl Handbag Pink Shoulder YO Cheap Large rqZYwr1
Messenger Quilted Italian Designer Orlandi Leather Valentino Bag Burgundy Purse
Orlandi Messenger Quilted Leather Italian Bag Purse Valentino Burgundy Designer Orlandi Leather Valentino Messenger Burgundy Bag Purse Quilted Italian Designer

Purse Valentino Italian Designer Quilted Burgundy Orlandi Bag Messenger Leather wZgRxZSpn

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: Orlandi Leather Burgundy Italian Bag Valentino Purse Designer Messenger Quilted collapse_samples.py [options]

Input Arguments:

Purse Designer Quilted Italian Burgundy Valentino Orlandi Messenger Bag Leather Note

[REQUIRED]

-b, -on LA'FESTIN Handbags Fashion Off Clearance White Shoulder 1qqxS0T8002 Leather Bag Black Purses 8003 CrossBody Bag Designer Women's PIJUSHI Summer Shoulder Genuine qUZZwO-input_biom_fp
The biom table containing the samples to be collapsed
Tote Handbag Head Black Canvas Wolf Hand Bag Blue Women's Shoulder Large ZEO6nqwC
-m, --mapping_fp
The sample metdata mapping file
Handbag Functional Hobo Baggallini Tote Charcoal Crossbody Pockets wx8WAFq
--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]
Crossbody Nine West Small Elm Tunnel aazqxt
--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 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