process_input {htrSPRanalysis} | R Documentation |
Process user input files and obtain options for fitting.
Description
Performs all functions selected in sample information, such as automated dissociation window detection, automated concentration range, automated bulk shift detection and returns a list object with the titration time series, processed sample information, all user inputs directing file outputs and fitting options
Usage
process_input(
sample_sheet_path = NULL,
data_file_path = NULL,
output_file_path = NULL,
output_pdf = NULL,
output_csv = NULL,
error_pdf = NULL,
num_cores = NULL,
min_allowed_kd = 10^(-5),
max_iterations = 1000,
ptol = 10^(-10),
ftol = 10^(-10),
min_RU_tol = 20,
max_RU_tol = 300
)
Arguments
sample_sheet_path |
The full path to the sample information file. |
data_file_path |
The full path to the titration data file. |
output_file_path |
The full path where output should be stored. This directory needs to exist. |
output_pdf |
The name of the file for the pdf output. |
output_csv |
The name of the file for the csv output. |
error_pdf |
The name of the file for error output. |
num_cores |
The number of cores to use for parallel processing. The default is( the number of cores detected by |
min_allowed_kd |
The minimum value for the dissociation constant. The default is 10^(-5). |
max_iterations |
The maximum number of iterations for curve fitting. The default is 1000. |
ptol |
Curve fitting parameter. If the proposed changes in parameters is smaller than this value, the optimization is considered converged. The default is 10^(-10) |
ftol |
Curve fitting parameter. If the squared error between observed and predicted values is smaller than ftol, the optimization is considered converged. The default is 10^(-10) |
min_RU_tol |
Minimum RU required for dissociation window detection |
max_RU_tol |
Maximum RU required for dissociation window detection. Also used in curve fitting. |
Value
A list object containing the following
expanded_sample_sheet |
The sample sheet expanded to include all spots that are represented, expanding the short-hand entries for Position/Block/Channel |
sample_info |
The expanded sample sheet with only the rows that are to be fit |
sample_info_fits |
The sample_info without rows that have encountered errors in initial processing |
Time |
The dataframe whose columns are the Time values for the input titration data. This only includes columns selected for analysis. |
RU |
The dataframe whose columns are the RU values for the input titration data. Only the columns for the samples to be analyzed are included |
correctedRU |
The |
keep_concentrations |
A vector containing the indices of the columns from |
all_concentrations_values |
A vector containing the concentration values corresponding to the columns of the |
incl_concentrations_values |
A vector containing the concentration values corresponding to the |
n_time_points |
The maximum length of titration time series |
max_RU_tol |
The maximum RU for dissociation window trimming to be automated |
min_RU_tol |
The minimum RU for dissociation window trimming to be automated |
min_RU_tol |
The minimum RU for dissociation window trimming to be automated |
nwells |
The number of rows in the |
n_fit_wells |
The number of rows in the |
ftol |
The ftol parameter passed to the |
ptol |
The ptol parameter passed to the |
ptol |
The ptol parameter passed to the |
output_pdf |
The full pathname for the output pdf file |
output_csv |
The full pathname for the output csv file |
error_pdf |
The full pathname for the pdf error file. This is where errors in processing can be found. |
error_idx_concentrations |
If there is an issue in determining the concentration window for some spots, they will be logged here |
Examples
# set up file paths for example
sample_sheet_path <- system.file("extdata",
"sample_sheet.xlsx", package="htrSPRanalysis")
fn <- paste0("https://gitlab.oit.duke.edu/janice/htrspranalysis/",
"-/raw/master/inst/extdata/titration_data.xlsx?ref_type=heads")
download.file(fn,
destfile = paste0(tempdir(),"/titration_data.xlsx"),
mode = "wb")
data_file_path <- paste0(tempdir(), "/titration_data.xlsx")
# process the input
processed_input <- process_input(sample_sheet_path = sample_sheet_path,
data_file_path = data_file_path,
num_cores = 2)