read.files: read.files - Function to read data from CSV or FCS files into...
In ImmuneDynamics/Spectre: High-dimensional cytometry and imaging analysis

read.files

R Documentation

read.files - Function to read data from CSV or FCS files into a list.

Description

This function allows you to read in sample files (.csv or .fcs) into a list, where each file is saved as a data.table.

Usage

read.files(file.loc, file.type, do.embed.file.names, header)

Arguments

`file.loc`	DEFAULT = getwd(). What is the location of your files?
`file.type`	DEFAULT = ".csv". What type of files do you want to read. Can be ".csv" or ".fcs".
`files`	DEFAULT = NULL. A vector of selected file names to import.
`nrows`	DEFAULT = NULL. Can specify a numerical target for the number of cells (rows) to be read from each file. Please note, order is random in FCS files.
`do.embed.file.names`	DEFAULT = TRUE. Do you want to embed each row (cell) of each file with the name name?
`header`	DEFAULT = TRUE. Does the first line of data contain column names?

Value

Returns a list of data.tables – one per CSV file.

Author(s)

Thomas M Ashhurst, thomas.ashhurst@sydney.edu.au Felix Marsh-Wakefield, felix.marsh-wakefield@sydney.edu.au

References

Ashhurst, T. M., et al. (2019). https://www.ncbi.nlm.nih.gov/pubmed/31077106

Examples

# download sample data
download.file(url='https://github.com/ImmuneDynamics/data/blob/main/msCNS.zip?raw=TRUE', destfile = 'msCNS.zip', mode = 'wb')
unzip(zipfile = 'msCNS.zip')
setwd("msCNS/data")
data.list <- read.files(file.type = ".csv", do.embed.file.names = TRUE)

# return to previous working directory
setwd("../../")

ImmuneDynamics/Spectre documentation built on Oct. 12, 2024, 7:55 p.m.