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

In YAPSA: Yet Another Package for Signature Analysis

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

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:

• vcf_like_df_list: List of the read data frames

• readVcf_time: Object of class proc_time, which stores the time needed for reading in the data

Examples

 NULL

 NULL

YAPSA documentation built on Nov. 8, 2020, 4:59 p.m.