Description Usage Arguments Details Author(s) References Examples
This function merges mapping file metadate (mapping file information formatted according to Qiime specifications) with dataset output from Qiime, including alpha diversity, bacterial relative abundance, and bacterial load (this must be aquired outside of standard Qiime sequencing methods). Merge the necessary mapping file columns (subject ID and time point which could be days, etc) into the datasets for alpha diversity, bacterial load, and taxa relative abundance.
1 2 3 4 5 6 7 8 9 | mergeMapMetaData(map.file,
merging.file,
map.sub.id="SubjectID",
map.tmpt="Time_point",
map.smpl.id="SampleID",
merge.smpl.id,
sample.id.col="SampleID",
subject.id.col="SubjectID",
tmpt.id.col="Time_point")
|
map.file |
The mapping file |
merging.file |
The |
map.sub.id |
Name of the subject ID column found in the Qiime mapping file. Default is "SubjectID". |
map.tmpt |
Name of the time point column found in the Qiime mapping file. Default is "Time_point". |
map.smpl.id |
Name os the sample ID column found in the Qiime mapping file. Default is "SampleID". |
sample.id.col |
Desired name of the Sample ID column for the final merged |
subject.id.col |
Desired name of the Subject ID column for the final merged |
tmpt.id.col |
Desired name of the Time Point column for the final merged |
merge.smpl.id |
Desired name of the sample ID column in the file to be merged with. This has no default. |
Package: | patPRO |
Type: | Package |
Version: | 1.0.0 |
Date: | 2015-09-18 |
License: | GPLv3 |
An overview of how to use the package, including the most important functions, is included in the supplemental R notebook patPROExampleWorkflow.html.
Geoffrey Hannigan <ghanni@upenn.edu>, Loesche MA, Hodkinson BP, Mehta S, Elizabeth Grice <egrice@upenn.edu>
patPRO: An R package for the visualization of longitudinal microbiome data. Hannigan GD, Loesche MA, Hodkinson BP, Mehta S, Grice EA.
1 2 3 4 5 6 7 8 9 10 | library("patPRO")
data("PatProOTU",package="patPRO")
data("PatProMap",package="patPRO")
transTestRelAbund <- transposeRelAbund(PatProOTU)
mergedMapTransRA <- mergeMapMetaData(map.file=PatProMap,
merging.file=transTestRelAbund,
map.sub.id="SubjectID",
map.tmpt="Time_point",
map.smpl.id="SampleID",
sample.id.col="SampleID")
|
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