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 - 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".
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, [e-mail] Felix Marsh-Wakefield, [e-mail]

References

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

Examples

data.list <- read.files(file.loc = getwd(), file.type = ".csv", do.embed.file.names = TRUE)

ImmuneDynamics/Spectre documentation built on Nov. 12, 2023, 8:12 a.m.