Create a table for defining dataset annotations

To process an entire dataset, we need a table that describes the samples, and you may want to add for the analysis.

create_annotations_table(
  samples_dir,
  glob = c("*.mea", "*.mea.gz"),
  recursive = TRUE,
  verbose = TRUE
)

Arguments

samples_dir

A directory that contains samples

glob

One or more globs for sample extensions. See the examples.

recursive

Whether to look for samples into samples_dir subdirectories

verbose

If set to TRUE it prints instructions

Value

A data frame with the SampleID and FileName columns

Details

The table needs to have at least two columns, one with the file name of the sample (FileName) and another one with the sample name (SampleID), that you can set as you like. Besides, you can add additional columns with any metadata/annotations/phenotypes you may consider relevant.

This function will help you list all the samples from a directory to a table. The example below will show you how to save this table as an Excel or CSV file, for you to conveniently modify it and how you can read it back for further analysis.

Examples

# How to create the annotations table:
#
# First you must tell R where your samples are. Please change "samples_dir"
# below to your samples directory. On Windows you can use:
#     samples_dir <- choose.dir(getwd(), "Choose the folder where the samples are")
# On other systems you can use:
#     library(tcltk)
#     samples_dir <- tclvalue(tkchooseDirectory())
# In this example we use a folder with some demo files:
samples_dir <- system.file("extdata", "sample_formats", package = "GCIMS")
# Then you need to provide the extension to look into. If you use `glob = "*.*"` you
# will catch all files and you can filter the annotations table afterwards:
annotations <- create_annotations_table(samples_dir, glob = "*.mea.gz")
#> An annotation table was created
#> ℹ The table now includes 1 samples
#> ℹ Feel free to edit the table to include additional annotations as extra
#>   columns (for groups, phenotypes...), please avoid renaming the SampleID and
#>   FileName columns
#> ℹ You may freely add/remove rows to include/exclude additional samples
#> ℹ For editing, you can do it from R or you can check the examples at
#>   `help("create_annotations_table")` tolearn how to save the table to an Excel
#>   file at your convenience
# You can write the annotations table to an Excel or a CSV file:
# For Excel you may need to install the writexl package:
#    install.packages("writexl")
# And then you can use:
#    writexl::write_xlsx(annotations, "annotations.xlsx")
# For csv just use:
#    write.csv(annotations, "annotations.csv")
#
# Modify manually the excel or CSV file
#
# Read it again into R as follows:
#
# For Excel you may need to install the readxl package:
#    install.packages("readxl")
# And then you can use:
#    annotations <- readxl::read_excel("annotations.xlsx")
# For csv just use:
#    annotations <- read.csv("annotations.csv")