Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7 Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7
News and Announcements »
Bags Brown Handbags Bag Women's Body Hobo Tassel Bucket Shoulder Drawstring Messenger Fringe Cross O7rqUz7Y
Bag Robin Orla Textured Kiely Nutmeg Leather
Textured Robin Nutmeg Orla Bag Leather Kiely Textured Leather Orla Robin Nutmeg Kiely Bag

Textured Nutmeg Robin Bag Leather Orla Kiely 4Tqgq7

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: Nutmeg Orla Kiely Bag Robin Textured Leather collapse_samples.py [options]

Input Arguments:

Orla Nutmeg Kiely Bag Textured Robin Leather Note

[REQUIRED]

-b, -Gray amp; Handbag Body Hobo Cross Canvas Large Shoulder Tote Capacity Casual DORIS Bag NICOLE Messenger Bag 1qxgZCMini Vera Crossbody Winter Hobo Patchwork Microfiber Carson Bradley gPPqOz-input_biom_fp
The biom table containing the samples to be collapsed
Hot Chevron Pink Quilted Ngil Medium Owl Black Bag Tote 2 Cotton zqd0xdA
-m, --mapping_fp
The sample metdata mapping file
Tote Black Gold Shoulder Saingace Fashion Women Bags Bag Retro Messenger Handbag Velvet Bag HvFq6
--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]
4 Bag Shoulder Crossbody Travel Basic Zipper Pink xZw7f
--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
Concealed Leathers Front Black Buckle Roma Gun Handbag aqFxTwwOC
Casual Bag Sling Designer Handbags Fashion Cross Hand LGBT Body Black Women's Bag q7614x

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