getReadsPage {GoogleGenomics} | R Documentation |
In general, use the getReads method instead. It calls this method, returning reads from all of the pages that comprise the requested genomic range.
getReadsPage(readGroupSetId = "CMvnhpKTFhDnk4_9zcKO3_YB", chromosome = "22", start = 16051400, end = 16051500, fields = NULL, pageToken = NULL)
readGroupSetId |
The read group set ID. |
chromosome |
The chromosome. |
start |
Start position on the chromosome in 0-based coordinates. |
end |
End position on the chromosome in 0-based coordinates. |
fields |
A subset of fields to retrieve. The default (NULL) will return all fields. |
pageToken |
The page token. This can be NULL (default) for the first page. |
By default, this function gets reads for a small genomic region for one sample in 1,000 Genomes.
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:
A two-element list is returned by the function.
reads: A list of R objects corresponding to the JSON objects returned by the Google Genomics Reads API.
nextPageToken: The token to be used to retrieve the next page of results, if applicable.
Other page fetch functions: callGRPCMethod
,
getSearchPage
,
getVariantsPage
# Authenticated on package load from the env variable GOOGLE_API_KEY. readsPage <- getReadsPage() summary(readsPage) summary(readsPage$reads[[1]])