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#' Create MS/MS search POST request body
#'
#' \code{create_msms_body} returns a string of a POST request body.
#'
#' @param ion_mass ion_mass
#' @param ms_ms_peaks ms_ms_peaks
#' @param precursor_ion_tolerance precursor_ion_tolerance
#' @param precursor_ion_tolerance_mode precursor_ion_tolerance_mode
#' @param precursor_mz_tolerance precursor_mz_tolerance
#' @param precursor_mz_tolerance_mode precursor_mz_tolerance_mode
#' @param ion_mode ion_mode
#' @param ionizationVoltage ionizationVoltage
#' @param spectra_types spectra_types
#'
#' @return If all inputs are all correctly formatted, a string of a POST request will be returned for the result.
#' @author Yaoxiang Li \email{yl814@georgetown.edu}
#'
#' Georgetown University, USA
#'
#' License: GPL (>= 3)
#' @export
#'
create_msms_body = function(ion_mass,
ms_ms_peaks,
precursor_ion_tolerance = 500.0,
precursor_ion_tolerance_mode = "mDa",
precursor_mz_tolerance = 1000.0,
precursor_mz_tolerance_mode = "mDa",
ion_mode = "positive",
ionizationVoltage = "all",
spectra_types = "experimental") {
ms_ms_peaks_vector <- c()
for (i in 1:nrow(ms_ms_peaks)) {
v <- paste0('{"mz":', ms_ms_peaks[i, 1],',"intensity":', ms_ms_peaks[i, 2],'}')
ms_ms_peaks_vector <- c(ms_ms_peaks_vector, v)
}
ms_ms_peaks_vector <- paste(ms_ms_peaks_vector, collapse = ",")
post_body <- paste0('{',
'"ion_mass":', as.character(ion_mass), ',',
'"ms_ms_peaks":[', ms_ms_peaks_vector, '],',
'"precursor_ion_tolerance":', as.character(precursor_ion_tolerance), ',',
'"precursor_ion_tolerance_mode":"', precursor_ion_tolerance_mode, '",',
'"precursor_mz_tolerance":', as.character(precursor_mz_tolerance), ',',
'"precursor_mz_tolerance_mode":"', precursor_mz_tolerance_mode, '",',
'"ion_mode":"', ion_mode, '",',
'"ionizationVoltage":"',ionizationVoltage, '",',
'"spectra_types":["experimental","predicted"]',
'}')
}
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