loadSmallRnaRun: Load small RNA-seq bcbio-nextgen run
In lpantano/bcbioSmallRna: small RNA-Seq Utilities

Description Usage Arguments Value Note Author(s) Examples

Simply point to the final upload directory output by bcbio-nextgen, and this function will take care of the rest. It automatically imports small RNA-seq counts, metadata, and program versions used.

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loadSmallRnaRun(projectDir = "date-final",
  interestingGroups = "sample", maxSamples = 50, minHits = 5,
  dataDir = NULL, colData = NULL, ...)

`projectDir`	Path to final upload directory. This path is set when running `bcbio_nextgen -w template`.
`interestingGroups`	Character vector of interesting groups. First entry is used for plot colors during quality control (QC) analysis. Entire vector is used for PCA and heatmap QC functions.
`maxSamples`	Optional. Maximum number of samples to calculate rlog and variance stabilization object from DESeq2.
`minHits`	Optional. Minimum lines to have in the miRNA output to load the sample.
`dataDir`	Folder to keep a cache of the object.
`colData`	Optional External metadata to be used while reading samples.
`...`	Additional arguments, saved as metadata.

bcbioSmallRnaDataSet.

When working in RStudio, we recommend connecting to the bcbio-nextgen run directory as a remote connection over sshfs.

Michael Steinbaugh, Lorena Pantano

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path <- system.file("extra", package="bcbioSmallRna")
sbcb <- loadSmallRnaRun(file.path(path, "geu_tiny", "final",
                                  "2018-12-05_geu_tiny"), "population")