Coverage {BaseSpaceR} | R Documentation |
This methods are used to provide mean read coverage depth in a particular chromosomal region.
getCoverageStats(x, ...) getCoverage(x, ...)
x |
An object of class |
... |
Adiditional arguments supported by the REST API.
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Coming soon...
These methods return a list with a representation of coverage histogram.
Adrian Alexa
https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference
data(aAuth) ## get the Ids of some BAM files ##... ## You might require Read access to the AppResult #initializeAuth(aAuth, scope = paste("browse global, read project", 12)) #requestAccessToken(aAuth) #getCoverageStats(aAuth, id = bid, "phix") #readcov <- getCoverage(aAuth, id = bid, "phix", StartPos = 1L, EndPos = 5e3L)[[1]] #barplot(readcov$MeanCoverage, col = "lightblue1", border = NA) #plot(readcov$MeanCoverage, col = "lightblue2", type = "l", lwd = 2)