fread_rownames: Use 'fread()' to read a csv/tsv with row names (e.g. one...

In tanaylab/tgutil: Simple utility functions for Tanay lab code

Use 'fread()' to read a csv/tsv with row names (e.g. one created with 'write.table()')

Description

Use 'fread()' to read a csv/tsv with row names (e.g. one created with 'write.table()')

Usage

fread_rownames(..., row.var = "rowname")

Arguments

...

Arguments passed on to data.table::fread input A single character string. The value is inspected and deferred to either file= (if no \n present), text= (if at least one \n is present) or cmd= (if no \n is present, at least one space is present, and it isn't a file name). Exactly one of input=, file=, text=, or cmd= should be used in the same call. file File name in working directory, path to file (passed through path.expand for convenience), or a URL starting http://, file://, etc. Compressed files with extension ‘.gz’ and ‘.bz2’ are supported if the R.utils package is installed. text The input data itself as a character vector of one or more lines, for example as returned by readLines(). cmd A shell command that pre-processes the file; e.g. fread(cmd=paste("grep",word,"filename")). See Details. sep The separator between columns. Defaults to the character in the set [,\t |;:] that separates the sample of rows into the most number of lines with the same number of fields. Use NULL or "" to specify no separator; i.e. each line a single character column like base::readLines does. sep2 The separator within columns. A list column will be returned where each cell is a vector of values. This is much faster using less working memory than strsplit afterwards or similar techniques. For each column sep2 can be different and is the first character in the same set above [,\t |;], other than sep, that exists inside each field outside quoted regions in the sample. NB: sep2 is not yet implemented. nrows The maximum number of rows to read. Unlike read.table, you do not need to set this to an estimate of the number of rows in the file for better speed because that is already automatically determined by fread almost instantly using the large sample of lines. nrows=0 returns the column names and typed empty columns determined by the large sample; useful for a dry run of a large file or to quickly check format consistency of a set of files before starting to read any of them. na.strings A character vector of strings which are to be interpreted as NA values. By default, ",," for columns of all types, including type character is read as NA for consistency. ,"", is unambiguous and read as an empty string. To read ,NA, as NA, set na.strings="NA". To read ,, as blank string "", set na.strings=NULL. When they occur in the file, the strings in na.strings should not appear quoted since that is how the string literal ,"NA", is distinguished from ,NA,, for example, when na.strings="NA". stringsAsFactors Convert all or some character columns to factors? Acceptable inputs are TRUE, FALSE, or a decimal value between 0.0 and 1.0. For stringsAsFactors = FALSE, all string columns are stored as character vs. all stored as factor when TRUE. When stringsAsFactors = p for 0 <= p <= 1, string columns col are stored as factor if uniqueN(col)/nrow < p. verbose Be chatty and report timings? select A vector of column names or numbers to keep, drop the rest. select may specify types too in the same way as colClasses; i.e., a vector of colname=type pairs, or a list of type=col(s) pairs. In all forms of select, the order that the columns are specified determines the order of the columns in the result. drop Vector of column names or numbers to drop, keep the rest. colClasses As in utils::read.csv; i.e., an unnamed vector of types corresponding to the columns in the file, or a named vector specifying types for a subset of the columns by name. The default, NULL means types are inferred from the data in the file. Further, data.table supports a named list of vectors of column names or numbers where the list names are the class names; see examples. The list form makes it easier to set a batch of columns to be a particular class. When column numbers are used in the list form, they refer to the column number in the file not the column number after select or drop has been applied. If type coercion results in an error, introduces NAs, or would result in loss of accuracy, the coercion attempt is aborted for that column with warning and the column's type is left unchanged. If you really desire data loss (e.g. reading 3.14 as integer) you have to truncate such columns afterwards yourself explicitly so that this is clear to future readers of your code. integer64 "integer64" (default) reads columns detected as containing integers larger than 2^31 as type bit64::integer64. Alternatively, "double"|"numeric" reads as utils::read.csv does; i.e., possibly with loss of precision and if so silently. Or, "character". dec The decimal separator as in utils::read.csv. If not "." (default) then usually ",". See details. check.names default is FALSE. If TRUE then the names of the variables in the data.table are checked to ensure that they are syntactically valid variable names. If necessary they are adjusted (by make.names) so that they are, and also to ensure that there are no duplicates. encoding default is "unknown". Other possible options are "UTF-8" and "Latin-1". Note: it is not used to re-encode the input, rather enables handling of encoded strings in their native encoding. quote By default ("\""), if a field starts with a double quote, fread handles embedded quotes robustly as explained under Details. If it fails, then another attempt is made to read the field as is, i.e., as if quotes are disabled. By setting quote="", the field is always read as if quotes are disabled. It is not expected to ever need to pass anything other than \"\" to quote; i.e., to turn it off. strip.white default is TRUE. Strips leading and trailing whitespaces of unquoted fields. If FALSE, only header trailing spaces are removed. fill logical (default is FALSE). If TRUE then in case the rows have unequal length, blank fields are implicitly filled. blank.lines.skip logical, default is FALSE. If TRUE blank lines in the input are ignored. index Character vector or list of character vectors of one or more column names which is passed to setindexv. As with key, comma-separated notation like index="x,y,z" is accepted for convenience. Only valid when argument data.table=TRUE. Where applicable, this should refer to column names given in col.names. showProgress TRUE displays progress on the console if the ETA is greater than 3 seconds. It is produced in fread's C code where the very nice (but R level) txtProgressBar and tkProgressBar are not easily available. nThread The number of threads to use. Experiment to see what works best for your data on your hardware. logical01 If TRUE a column containing only 0s and 1s will be read as logical, otherwise as integer. keepLeadingZeros If TRUE a column containing numeric data with leading zeros will be read as character, otherwise leading zeros will be removed and converted to numeric. yaml If TRUE, fread will attempt to parse (using yaml.load) the top of the input as YAML, and further to glean parameters relevant to improving the performance of fread on the data itself. The entire YAML section is returned as parsed into a list in the yaml_metadata attribute. See Details. autostart Deprecated and ignored with warning. Please use skip instead. tmpdir Directory to use as the tmpdir argument for any tempfile calls, e.g. when the input is a URL or a shell command. The default is tempdir() which can be controlled by setting TMPDIR before starting the R session; see base::tempdir. tz Relevant to datetime values which have no Z or UTC-offset at the end, i.e. unmarked datetime, as written by utils::write.csv. The default tz="UTC" reads unmarked datetime as UTC POSIXct efficiently. tz="" reads unmarked datetime as type character (slowly) so that as.POSIXct can interpret (slowly) the character datetimes in local timezone; e.g. by using "POSIXct" in colClasses=. Note that fwrite() by default writes datetime in UTC including the final Z and therefore fwrite's output will be read by fread consistently and quickly without needing to use tz= or colClasses=. If the TZ environment variable is set to "UTC" (or "" on non-Windows where unset vs ‘""' is significant) then the R session’s timezone is already UTC and tz="" will result in unmarked datetimes being read as UTC POSIXct. For more information, please see the news items from v1.13.0 and v1.14.0.

row.var

Name of column that will hold row names. Setting this parameter to NULL will maintain row names as row names.

tanaylab/tgutil documentation built on March 16, 2024, 12:07 a.m.