read_entry: Read a single vcf-like file into a single data frame

Description Usage Arguments Value Examples

View source: R/io_functions.R

Description

Note: this function uses read.csv to read vcf-like files into data frames for single samples. As it uses read.csv, the default value for comment.char is "" and not "#" as it would have been for read.table.

Usage

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read_entry(
  current_ind,
  in_list,
  header = TRUE,
  in_header = NULL,
  variant_type = "SNV",
  delete.char = NULL,
  ...
)

read_list(in_list, in_parallel = FALSE, header = TRUE, in_header = NULL, ...)

Arguments

current_ind

Index of the file to read from the list provided below.

in_list

List of paths to vcf-like file to be read. The list may be named.

header

Boolean whether a header information should be read (as in read.table)

in_header

Vector of column names to be substituted if non-NULL.

variant_type

Default is "SNV" and provides additional plausibility and checks, omitted if other string

delete.char

Character to be deleted, e.g. in order to discriminate between comment lines and header lines, if non-NULL

...

Parameters passed on to read.table

in_parallel

If multicore functionality is provided on a compute cluster, this option may be set to TRUE in order to enhance speed.

Value

A vcf-like data frame

A list with entries:

Examples

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slw287r/yapsa documentation built on June 7, 2020, 12:46 a.m.