metaData: Container for metadata.
In anabeloff/AODPvisual: AODP data visualisation
Description
Usage
Arguments
Details
Author(s)
Description
This functions takes metadata table and original sequences. It creates list of these objects and calculates total number of sequences in each sample.
Usage
1
Arguments
metadata
Dataframe with metadata. Column 'ID' must contain sample IDs.
sequence_totals
Data.frame containing two columns: sample IDs and number of sequences per ID. Or path to FASTA file containing the same sequences used in AODP matching as 'Target'.
aodp_match
Path to AODP match file or output of readAODPmatch() function.
value
Cutoff value (numeric) for AODP match persentage identity. Default 99
species_number
Cutoff Species number (numeric) for AODP match. This defines maximum number of Sprcies (column) assined to one sequence (column: seq_ID).
Details
metaData() function creates a combined list with four dataframes:
Metadata - table with meta data information;
Sample_totals - IDs total sequence count table;
AODP_match - AODP match table (if specified).
Author(s)
Anatoly Belov
anabeloff/AODPvisual documentation built on May 16, 2019, 6:56 p.m.
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Description Usage Arguments Details Author(s)
Description
This functions takes metadata table and original sequences. It creates list of these objects and calculates total number of sequences in each sample.
Usage
1 |
Arguments
metadata |
Dataframe with metadata. Column 'ID' must contain sample IDs. |
sequence_totals |
Data.frame containing two columns: sample IDs and number of sequences per ID. Or path to FASTA file containing the same sequences used in AODP matching as 'Target'. |
aodp_match |
Path to AODP match file or output of readAODPmatch() function. |
value |
Cutoff value (numeric) for AODP match persentage identity. Default 99 |
species_number |
Cutoff Species number (numeric) for AODP match. This defines maximum number of Sprcies (column) assined to one sequence (column: seq_ID). |
Details
metaData() function creates a combined list with four dataframes: Metadata - table with meta data information; Sample_totals - IDs total sequence count table; AODP_match - AODP match table (if specified).
Author(s)
Anatoly Belov
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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