Read and aggregate genomic or non-genomic data files with smart format detection

Collect all files that match a specific pattern at a specific path, detect the file format, use the appropriate reader function, then aggregate into a single data.table. Automatically detects and handles BED, BEDPE, MAF, VCF, and generic tabular formats. All files are read as data.tables and aggregated, ensuring maximum compatibility and performance.

Usage

aggregate_these(
  path_to_files,
  pattern_to_grab,
  file_format = c("auto", "bed", "bedpe", "maf", "vcf", "generic"),
  delim = "auto",
  has_header = TRUE,
  cpus = 1,
  add_uniq_id = FALSE,
  id_column_name = "sample_id",
  verbose = TRUE,
  ...
)

Arguments

path_to_files

Path to location of files to be aggregated

pattern_to_grab

Pattern (regex) used to identify files

file_format

Character string to force specific format detection: "auto" (default), "bed", "bedpe", "maf", "vcf", "generic". Default: "auto"

delim

Delimiter for generic files. Default: "auto"

has_header

Logical, if files have header line. Default: TRUE

cpus

Number of CPUs for reading data. Default: 1

add_uniq_id

Logical, add unique identifier column from filename. Default: FALSE

id_column_name

Character, name for unique identifier column. Default: "sample_id"

verbose

Logical, print progress messages. Default: TRUE

...

Additional arguments passed to format-specific readers

Value

data.table object with aggregated data from all files