Create sample description table containing all required inputs
Each sample will have a unique name along with a pair of CNA and gene expression file. This function generates a table of sample descriptions by either reading an external CSV file or specifying them through separate arugments in same order.
external sample description CSV file having at
least these three columns:
character vector of distinct sample names. Samples will be referenced by the given name through out the analysis process. They should be valid R data.table column names.
character vector of filepaths to CNA data.
character vector of filepaths to gene expression data.
path to the root of sample data. If given, this path will be appended before all given filepaths.
data.table of sample description having the following columns in
GE_filepath. Each row
contains a sample's unique name and the corresponding filepaths to CNA and
gene expression data.
One could convert the relative file paths into absolute paths by
passing the root folder path to
If for some special reasons, for example gene expression of all samples
have been collected or the CNA records for each gene exist, but do not have
the file paths to either CNA or gene expression data, pass it with empty
character vector of correct length, such as
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
## Custom sample description by specifying separate arguments sample_names <- letters[1:5] sample_desc <- create_sample_desc( sample_names = sample_names, cna_filepaths = file.path('cna', paste0(sample_names, '.csv')), ge_filepaths = file.path('ge', paste0(sample_names, '.txt')) ) sample_desc ## Prepend the file path with a root directory /path/to/sample create_sample_desc( sample_names = sample_desc$Sample, cna_filepaths = sample_desc$CNA_filepath, ge_filepaths = sample_desc$GE_filepath, sample_root = '/path/to/sample' ) ## Create by reading a sample description CSV file sample_desc_pth <- system.file("extdata", "sample_desc.csv", package = "iGC") sample_desc <- create_sample_desc(sample_desc_pth) ## Not run: ## Read a external description and append the given file paths create_sample_desc('/path/to/desc.csv', sample_root='/path/to/sample/root') ## End(Not run)
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