trim {strvalidator}

Trim Data

Description

Extract data from a dataset.

Usage

trim(
  data,
  samples = NULL,
  columns = NULL,
  word = FALSE,
  ignore.case = TRUE,
  invert.s = FALSE,
  invert.c = FALSE,
  rm.na.col = TRUE,
  rm.empty.col = TRUE,
  missing = NA,
  debug = FALSE
)

Arguments

data

data.frame with genotype data.

samples

string giving sample names separated by pipe (|).

columns

string giving column names separated by pipe (|).

word

logical indicating if a word boundary should be added to samples and columns.

ignore.case

logical, TRUE ignore case in sample names.

invert.s

logical, TRUE to remove matching samples from 'data', FALSE to remove samples NOT matching (i.e. keep matching samples).

invert.c

logical, TRUE to remove matching columns from 'data', FALSE to remove columns NOT matching (i.e. keep matching columns). while TRUE will remove columns NOT given.

rm.na.col

logical, TRUE columns with only NA are removed from 'data' while FALSE will preserve the columns.

rm.empty.col

logical, TRUE columns with no values are removed from 'data' while FALSE will preserve the columns.

missing

value to replace missing values with.

debug

logical indicating printing debug information.

Details

Simplifies extraction of specific data from a larger dataset. Look for samples in column named 'Sample.Name', 'Sample.File.Name', or the first column containing the string 'Sample' in mentioned order (not case sensitive). Remove unwanted columns.

Value

data.frame with extracted result.