#' Identify cross-linked peptides from open modification searches.
#'
#'#' @include xlinkTbl.R
.xcombr_interpret <- function(PSMs,
xlSpecificity = NULL,
xlMass = NULL,
customSpecificity = NULL,) {
# Define valid arg values --------------------------------------------------
xlSpecificityValues <- c(xlinkTbl$name, "custom", NULL)
# Check args ---------------------------------------------------------------
.checkArgsInterpret(xlSpecificity,
xlMass,
customSpecificity,
# possible values for arguments:
xlSpecificityValues)
# Find Candidate XL PSMs ---------------------------------------------------
# Automatically determine xlMass --------------------------------------------
# (uses distribution of precursor mass defects from candidate XL PSMs)
}
# Argument Checking
.checkArgsInterpret <- function(xlSpecificity,
xlMass,
customSpecificity,
xlSpecificityValues){
# xlSpecificity
if(!is.null(xlSpecificity)) {
if(!is.character(xlSpecificity) |
length(xlSpecificity) != 1) {
stop("xlSpecificity must be a character vector of length 1 or NULL")
} else if(!(tolower(xlSpecificity) %in% tolower(xlSpecificityValues))) {
stop("Unrecognized xlSpecificity. Refer to xcombr_specificities() for options.")
}
}
# xlMass
if(!is.null(xlMass)) {
if(length(xlMass) != 1 ||
!is.numeric(minLength) ||
minLength < 0) {
stop("minLength must be a single positive integer value or NULL")
}
}
#customSpecificity
if(tolower(xlSpecificity == "custom")) {
if(is.null(customSpecificity)) {
stop("customSpecificity is required when xlSpecificity = 'custom'.")
} else if(!is.character(customSpecificity) |
length(customSpecificity) != 2) {
stop("customSpecificity must be a character vector of length 2.")
}
}
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.