R: Read various input file formats into a list of data frames....

read.to.list

R Documentation

Read various input file formats into a list of data frames. Wrapper function for 'read2list' to automate reading further and avoid errors due to missing folders or files.

Description

read.to.list is meant to act as a universal reading function as it attempts to read a number of different file formats into a list of data frames.

Usage

read.to.list(
  dat,
  type,
  folder,
  nsheets = 1,
  sheet = NULL,
  keep.tibble = FALSE,
  skip = 0,
  sep = NULL,
  lines = FALSE,
  dec = NULL,
  ...,
  verbose = TRUE,
  x.verbose = FALSE
)

Arguments

`dat`	`character`. File path.
`type`	`character`. File extension to be read: one of ".txt", ".tsv", ".csv", ".vcf", ".gtf", ".gff", ".xls", ".xlsx", ".xdr", ".RData", ".rds", ".rda", ".xml". See details.
`folder`	`character`. Folder where the file is found.
`nsheets`	`integer`. Number of sheets to be read if file is of type ".xls" or ".xlsx". All sheets starting from 1 up to the given number in the respective data file will be read. If more than one file is read this must be be an integer vector with the numbers of sheets in exactly the same order as the files.
`sheet`	`integer` or `list`. Sheet(s) to be read if file is of type ".xls" or ".xlsx". The sheets defined by the given integer in the respective data file will be read. If more than one file is read this must be be a list with the sheet number(s) in exactly the same order as the files. If there are many files and only one sheet vector the same sheet(s) wiÃ¶l be read from all files.
`keep.tibble`	`logical`. Should the data from Excel files read with `readxl::read_excel` be coerce to `data.frames` or kept in the original `tibble` format? Defaults to FALSE, i.e., a `data.frame` is returned.
`skip`	`integer`. Number of lines to skip from the top of the file.
`sep`	`character`. Field delimiter passed to 'read.delim' when reading text files.
`lines`	`lines`. Should the file be read line by line into a character vector by readLines()?
`dec`	`character`. The decimal separator for numbers.
`...`	Additional arguments passed to functions.
`verbose`	`logical`. Should verbose output be printed?
`x.verbose`	`logical`. Should extended verbose output be printed?

Details

Excel files (file extension .xls or .xlsx) will be read by readxl::read_excel. A test is attempted to determine whether the input file is genuinely derived from Excel or only named like an nExcel file. If the latter, it will be attempted to read it as text file. Text files are read as tables or by line if lines is TRUE. For text files, field delimiters and decimal separators are determined automatically if not provided. Files with the extensions .txt", ".tsv", ".csv", ".gtf" and ".gff" are treated and read as text files. VCF files are also treated as text files but can noly be read in full (incl. header) if read by line. Otherwise, if skip is 0, the line with the column names will be determined automatically and the file read as delimited text file. XML files are read by xml2::read_xml. ".RData" files are loaded and assigned a name. ".rds" and ".rda" files are read by readRDS. ".xdr" files are read by R.utils::loadObject.

Value

A list of tibbles/data frames.

Examples

# The function readxl::read_excel is used internally to read Excel files.
# The example used their example data.
readxl_datasets <- readxl::readxl_example("datasets.xlsx")
# A randomly generated data frame was saved to a tab-separated text file
# and two different R object files.
tsv_datasets <- dir(system.file("extdata", package = "readmoRe"), full.names = TRUE)
# All example data are read into a list. From the Excel file, the first
# sheet is read.
dat <- read.to.list(c(readxl_datasets, tsv_datasets))
# All example data are read into a list. From the Excel file, the first
# 3 sheets are read.
dat <- read.to.list(c(readxl_datasets, tsv_datasets), nsheets=3)
# All example data are read into a list. From the Excel file, sheets 1 and
# 4 are read.
dat <- read.to.list(c(readxl_datasets, tsv_datasets), sheet=c(1, 4))
# From two Excel files, different sheets are read: 1 and 4 from the first
# file and 2 and 3 from the second.
# (For simplicity, the same example file is used.)
dat <- read.to.list(c(readxl_datasets, readxl_datasets), sheet=list(c(1, 4), c(2, 3)))