readsToGAlignments {GoogleGenomics} | R Documentation |
Note that the Global Alliance for Genomics and Health API uses a 0-based coordinate system. For more detail, please see GA4GH discussions such as the following:
readsToGAlignments(reads, oneBasedCoord = TRUE, slStyle = "UCSC")
reads |
A list of R objects corresponding to the JSON objects returned by the Google Genomics Reads API. |
oneBasedCoord |
Convert genomic positions to 1-based coordinates. |
slStyle |
The style for seqnames (chrN or N or...). Default is UCSC. |
# Authenticated on package load from the env variable GOOGLE_API_KEY. alignments1 <- getReads(converter=readsToGAlignments) summary(alignments1) alignments2 <- readsToGAlignments(getReads()) print(identical(alignments1, alignments2))