Coverage: Methods for accessing coverage data from BAM files

In BaseSpaceR: R SDK for BaseSpace RESTful API

Description

This methods are used to provide mean read coverage depth in a particular chromosomal region.

Usage

getCoverageStats(x, ...)
getCoverage(x, ...)

Arguments

x	An object of class AppAuth.
...	Adiditional arguments supported by the REST API. id File id (for a BAM file) within BaseSpace. chrom Character string given the chromosome name (UCSC).

Details

Coming soon...

Value

These methods return a list with a representation of coverage histogram.

Author(s)

Adrian Alexa

References

https://developer.basespace.illumina.com/docs/content/documentation/rest-api/api-reference

See Also

AppAuth.

Examples

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)

BaseSpaceR documentation built on Nov. 8, 2020, 5:12 p.m.