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

read_entry {YAPSA}

R Documentation

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

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

[Package YAPSA version 1.14.0 Index]