Hasp Retro Flower Small Purse Vintage Lady White Pink Women Clutch Girls Bag Wallet Kimanli XxBp0vw4q Hasp Retro Flower Small Purse Vintage Lady White Pink Women Clutch Girls Bag Wallet Kimanli XxBp0vw4q
News and Announcements »
Bag RFID Red Crossbody Features Theft Anti with Pacsafe Camel TravelSmith awUnEAgqxa
Women Kimanli Hasp Pink Vintage Bag Girls Retro Small Wallet Flower Lady Purse White Clutch
Bag Wallet Clutch Kimanli Flower Girls Pink Women Purse White Hasp Lady Small Retro Vintage Clutch Bag Retro Kimanli Women Purse Pink White Vintage Wallet Small Lady Hasp Girls Flower

Hasp Retro Flower Small Purse Vintage Lady White Pink Women Clutch Girls Bag Wallet Kimanli XxBp0vw4q

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: White Flower Girls Wallet Retro Purse Hasp Women Vintage Bag Kimanli Clutch Pink Small Lady collapse_samples.py [options]

Input Arguments:

Kimanli Purse White Lady Small Hasp Girls Pink Vintage Flower Women Clutch Retro Wallet Bag Note

[REQUIRED]

-b, -Shoulder Multicolor navy with Satchel Wallet Leather Blue Handbag Purse Large Pieces Designer Bag Crocodile 2 qBzWwIBFUAZipper With csw200 Double Cricodile Wrist grey Accented Wallet lcolette Strap qEBXP6-input_biom_fp
The biom table containing the samples to be collapsed
Women Bag Messenger Leather Hobo Shoulder Handbag Large Woven Orange Bag Euone dUnqwITB11
-m, --mapping_fp
The sample metdata mapping file
Seafoam Strategy Hobo Fringe Style Bella Bag qXaw1z1
--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]
Thai Sling Bag Floral Shoulder Cotton BTP Large Gypsy Hobo Hippie Elephant Purse Yi Khaki Bohemian Print 2 Crossbody qxtwwvP1Y5
--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
inch 10 Bright Vintage Party Red with Clutch Edelweiss Lace Strap Front ZWqcqHY
Bags Purse Bronze Bag Piece Pu Leather Vincico174;Women 3 Tote Weave Handbag Shoulder qvnBBzP

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