Coverage {BaseSpaceR}R Documentation

Methods for accessing coverage data from BAM files

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)


[Package BaseSpaceR version 1.26.0 Index]