scanTabix_to_dt: scanTabix to data.table

In RajLabMSSM/echotabix: echoverse module: automated creation and querying of tabix files

scanTabix to data.table

Description

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

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) 

RajLabMSSM/echotabix documentation built on Nov. 21, 2023, 8:02 a.m.