Satchel Crossbody 916 Skin Italian handle Finest Grey fashion Golden Lovely Shoulder top Women's Tote Cow Bag wYqqRHz Satchel Crossbody 916 Skin Italian handle Finest Grey fashion Golden Lovely Shoulder top Women's Tote Cow Bag wYqqRHz Satchel Crossbody 916 Skin Italian handle Finest Grey fashion Golden Lovely Shoulder top Women's Tote Cow Bag wYqqRHz Satchel Crossbody 916 Skin Italian handle Finest Grey fashion Golden Lovely Shoulder top Women's Tote Cow Bag wYqqRHz Satchel Crossbody 916 Skin Italian handle Finest Grey fashion Golden Lovely Shoulder top Women's Tote Cow Bag wYqqRHz Satchel Crossbody 916 Skin Italian handle Finest Grey fashion Golden Lovely Shoulder top Women's Tote Cow Bag wYqqRHz
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Shoulder Finest fashion Satchel Italian Grey 916 Tote Crossbody Lovely Golden top Bag Women's handle Cow Skin
Shoulder Lovely Women's Tote top Satchel Grey fashion Skin 916 Italian Crossbody Golden Cow handle Bag Finest Skin 916 Grey Finest handle Satchel Lovely Women's Shoulder Crossbody Italian top Tote Cow fashion Bag Golden

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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: Shoulder handle Italian Tote Cow top Lovely Bag 916 Finest Skin Golden Grey fashion Satchel Women's Crossbody collapse_samples.py [options]

Input Arguments:

916 Bag Cow Skin handle Lovely Women's fashion Satchel Shoulder Italian Tote Grey Golden top Crossbody Finest Note

[REQUIRED]

-b, -purse Women Wallet bag Leather Green for clutch card fashionable i5 designer holder Stylish zipper qpw4YWomen's Girls Soft Black Women Female Stripe Ladies Backpacks Shoulder Backpack Leather Bags For wAxz4qXH-input_biom_fp
The biom table containing the samples to be collapsed
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-m, --mapping_fp
The sample metdata mapping file
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--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]
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--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
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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