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scanTabix to data.table

Source: R/scanTabix_to_dt.R
scanTabix_to_dt.Rd

Convert the output of scanTabix into a data.table. Can handle tabix files that are missing column names, and query results that only have a single row.

Usage

scanTabix_to_dt(
  header,
  queries,
  add_query_names = TRUE,
  remove_duplicates = TRUE,
  sep = "\t",
  verbose = TRUE
)

Arguments

header

Header, from the output of headerTabix.

queries

A named list of query results, from the output of scanTabix.

add_query_names

Add the names of each query to a new column named 'query'.

remove_duplicates

Remove any duplicated rows. Set add_query_names=FALSE to prevent each unique range (e.g. SNP) from appearing in more than one row.

sep

The separator between columns. Defaults to the character in the set [,\t |;:] that separates the sample of rows into the most number of lines with the same number of fields. Use NULL or "" to specify no separator; i.e. each line a single character column like base::readLines does.

verbose

Print messages.

Examples

if (FALSE) { # \dontrun{
fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools",
                  mustWork=TRUE)
tbx <- Rsamtools::TabixFile(fl)

param <- GenomicRanges::GRanges(
    c("chr1", "chr2"),
    IRanges::IRanges(c(1, 1), width=100000))
queries <- Rsamtools::scanTabix(tbx, param=param)
header <- Rsamtools::headerTabix(fl)

#### Convert ####
query_dt <-  echotabix::scanTabix_to_dt(header = header,
                                        queries = queries)
} # }