db_to_granges: Convert an INSPIIRED database query into a GRanges object.
In cnobles/gintools: Genomic DNA Integration Analysis Tools

Description Usage Arguments Details Author(s) Examples

After querying data from an INSPIIRED integration site database, this function can convert the returned data.frame into a GRanges object given only the data.frame. The function generates a GRanges object containing the seqnames, starts, ends, and strands information as well as the sampleName and the specimen (parsed from the sampleName by the "-" delimiter). Additionally, if there are other data in columns of the data.frame, they can be transfered to the GRanges object by using the "keep.additional.columns = TRUE" option, but will be dropped if FALSE. Additional columns will be have there column names switched to lower case, but this feature can be turned off by using the option 'lower_case = FALSE'.

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db_to_granges(dfr_from_db)

db_to_granges(dfr_from_db, keep.additional.columns = TRUE, lower_case = TRUE)

`dfr_from_db`	a data.frame containing queried information from an INSPIIRED integration site database. Any data.frame can be used, but requires the columns: chr, position, breakpoint, strand, and sampleName.
`keep_additional_columns`	logical to specify whether to keep any columns besides those required in the data.frame.
`lower_case`	logical, default is TRUE. Changes additional column names to all lower case characters. FALSE leaves the additional column names as original format.
`split_sampleName`	logical, default is TRUE. Changes behavior of how to treat the sampleName column. If replicate information is not denoted by a "-#" at the end of the sampleName, then creating the specimen list will fail. Set to FALSE if replicate information is not included.

db_to_granges specifically converts a query from an INSPIIRED database to a GRanges object.

Christopher Nobles, Ph.D.

dfr <- data.frame(
  "chr" = c("chr1", "chr2", "chr2", "chr3"),
  "position" = c(5379927, 92775920, 2719573, 7195924),
  "breakpoint" = c(5380070, 92775995, 2719450, 7195890),
  "strand" = c("+", "+", "-", "-"),
  "sampleName" = c("GTSP0001-3", "GTSP0003-1", "GTSP0002-4", "GTSP0003-1"),
  "is.multihit" = c(FALSE, TRUE, FALSE, TRUE),
  stringsAsFactors = FALSE)

db_to_granges(dfr_from_db = dfr)

db_to_granges(dfr_from_db = dfr, keep_additional_columns = FALSE)