R/functions-mzR.R

In rformassspectrometry/PSM: Handling and Managing Peptide Spectrum Matches

##' A function to convert the identification data contained in an
##' `mzRident` object (as defined in the `mzR` package) to a
##' `data.frame`. Each row represents a scan, which can however be
##' repeated several times if the PSM matches multiple proteins and/or
##' contains two or more modifications.
##'
##' @details
##'
##' This function implements the same funtionality as `MSnbase::as(.,
##' "data.frame")`. It as been renamed and isn't been exported to
##' avoid conflicts and confusion. Ideally, the function in `MSnbase`
##' might be moved to `mzR` and this package would re-use that one.
##'
##' @title Coerce PSM data to a `data.frame`
##'
##' @param from An object of class `mzRident` as defined in the `mzR`
##'     package.
##'
##' @return A `data.frame`
##'
##' @author Laurent Gatto
##'
##' @importFrom BiocGenerics fileName
##'
##' @noRd
##'
##' @examples
##' ## find path to an mzIdentML file
##' f <- msdata::ident(full.names = TRUE, pattern = "TMT")
##' basename(f)
##'
##' library("mzR")
##' x <- openIDfile(f)
##' x
##' PSMatch:::as_data_frame(x)
as_data_frame <-
      function(from) {
          stopifnot(requireNamespace("mzR"))
          ## peptide spectrum matching
          iddf <- factorsAsStrings(mzR::psms(from))
          ## add file raw and mzid provenances
          src <- basename(mzR::sourceInfo(from))
          if (length(src) > 1) ## see issue #261
              src <- paste(src, collapse = ";")
          iddf$spectrumFile <- src
          iddf$idFile <- basename(fileName(from))
          ## add scores
          scores <- factorsAsStrings(mzR::score(from))
          if (nrow(scores)) { ## see issue #261
              stopifnot(identical(iddf[, 1], scores[, 1]))
              iddf <- cbind(iddf, scores[, -1])
          }
          ## add modification
          mods <- factorsAsStrings(mzR::modifications(from))
          names(mods)[-1] <- makeCamelCase(names(mods), prefix = "mod")[-1]
          iddf <- merge(iddf, mods,
                        by.x = c("spectrumID", "sequence"),
                        by.y = c("spectrumID",  "modSequence"),
                        suffixes = c("", ".y"),
                        all = TRUE, sort = FALSE)
          iddf[, "spectrumID.y"] <- NULL
          ## add substitutions
          subs <- factorsAsStrings(mzR::substitutions(from))
          names(subs)[-1] <- makeCamelCase(names(subs), prefix = "sub")[-1]
          iddf <- merge(iddf, subs,
                        by.x = c("spectrumID" = "sequence"),
                        by.y = c("spectrumID" = "subSequence"),
                        suffixes = c("", ".y"),
                        all = TRUE, sort = FALSE)
          iddf[, "spectrumID.y"] <- NULL
          iddf
      }


##' Convert a `vector` of characters to camel case by replacing dots
##' by captial letters.
##'
##' @title Convert to camel case by replacing dots by captial letters
##'
##' @param x A `character` to be transformed to camel case.
##'
##' @param prefix An optional `character` of length one. Any
##'     additional elements are ignores.
##'
##' @return A `character` of same length as `x`.
##'
##' @author Laurent Gatto
##'
##' @noRd
##'
##' @examples
##' nms <- c("aa.foo", "ab.bar")
##' PSMatch:::makeCamelCase(nms)
##' PSMatch:::makeCamelCase(nms, prefix = "x")
makeCamelCase <- function(x, prefix) {
    if (!missing(prefix))
        x <- paste(prefix[1], x, sep = ".")
    gsub('\\.(\\w?)', '\\U\\1', x, perl = TRUE)
}



##' This function produces the opposite as the `stringsAsFactors`
##' argument in the `data.frame` or `read.table` functions; it
##' converts `factors` columns to `characters`.
##'
##' @title Converts factors to strings
##'
##' @param x A `data.frame`
##'
##' @return A `data.frame` where `factors` are converted to
##'     `characters`.
##'
##' @author Laurent Gatto
##'
##' @noRd
##'
##' @examples
##' data(iris)
##' str(iris)
##' str(PSMatch:::factorsAsStrings(iris))
factorsAsStrings <- function(x) {
    x <- lapply(x,
                   function(xx) {
                       if (is.factor(xx)) as.character(xx)
                       else xx
                   })
    data.frame(x, stringsAsFactors = FALSE)
}