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Merge pull request #57 from margotbligh/dev
- add db matching - add utils - add annotation of ms2 fragment ions - move example_data to extdata
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| Original file line number | Diff line number | Diff line change |
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| #' Annotate m/z values of fragements in MS2 spectra from glycans | ||
| #' | ||
| #' @include setClass.R | ||
| #' @include glycoPredict.R | ||
| #' @include glycoAnnotate.R | ||
| #' | ||
| #' @description \code{glycoMS2Annotate()} annotates fragments in MS2 spectra | ||
| #' from precursors annotated as glycans by \link[GlycoAnnotateR]{glycoAnnotate}. | ||
| #' | ||
| #' @slot precursorAnnotations Vector of precursor annotations including IUPAC name, | ||
| #' ion and DP, separated by a colon (:) unless otherwise specified. Assumes | ||
| #' multiple annotations (if multiple annotations assigned to one precursor) are | ||
| #' separated by a comma! | ||
| #' @slot precursorAnnotations_sep Non-default separator of IUPAC name, ion and DP | ||
| #' in `precursorAnnotations` | ||
| #' @slot ms2spectra MS2 spectra from fragmentation of annotated precursors. MUST be | ||
| #' a dataframe with an 'mz' column for fragment ions and a 'precursorAnnotation' | ||
| #' column with precursor annotations (matching those in `precursorAnnotations`) | ||
| #' @slot ion_type Ionisation type. Currently accepted ESI and MALDI. Impacts ions. | ||
| #' @slot error Numeric value - error used to create window for matching. mz values | ||
| #' will be matched against theoretical mzs +- error. | ||
| #' @slot error_units Units for error - can be 'ppm' or 'Da' | ||
| #' @slot nmod_max Maximum number of modifications per monomer, calculated by the number of modifications over the number of monomers (default 1). | ||
| #' Does not take into account unsaturated, alditol or dehydrated. | ||
| #' @slot double_sulfate Logical. Can monomers be double-sulfated. If \code{TRUE}, nmod_max needs to have a value of at least 2. | ||
| #' @slot label Are sugars labelled by reductive amination? Current supported labels are: "none", "procainamide","2-aminobenzoic acid", | ||
| #' "2-aminobenzamide", "1-phenyl-3-methyl-5-pyrazolone". | ||
| #' | ||
| #' @export | ||
| #' | ||
| #' @seealso \link[GlycoAnnotateR]{glycoPredictParam} | ||
| #' @seealso \link[GlycoAnnotateR]{glycoPredict} | ||
| #' @seealso \link[GlycoAnnotateR]{glycoAnnotate} | ||
| #' @seealso \link[GlycoAnnotateR]{glycoMS2Extract} | ||
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| glycoMS2Annotate <- function(precursorAnnotations, | ||
| precursorAnnotations_sep = NULL, | ||
| ms2spectra, | ||
| error = 3, | ||
| error_units = 'ppm', | ||
| ion_type = 'ESI', | ||
| polarity = 'neg', | ||
| nmod_max = 1, | ||
| double_sulfate = FALSE, | ||
| label = 'none'){ | ||
| #check input validity | ||
| if(!is.vector(precursorAnnotations)){ | ||
| stop('precursorAnnotations is not a vector') | ||
| } | ||
| if(!all(grepl(':', precursorAnnotations)) & | ||
| is.null(precursorAnnotations_sep)){ | ||
| stop('No : separators in precursorAnnotations and no alternative provided') | ||
| } | ||
| if(!is.null(precursorAnnotations_sep)){ | ||
| if(!all(grepl(precursorAnnotations_sep, precursorAnnotations))){ | ||
| stop('No precursorAnnotations_sep in precursorAnnotations') | ||
| } | ||
| } | ||
| if(class(ms2spectra) != 'data.frame'){ | ||
| stop('ms2spectra is not a data.frame') | ||
| } | ||
| if(error_units != 'ppm' & error_units != 'Da'){ | ||
| stop('Error units are not ppm or Da') | ||
| } | ||
| if(!is.numeric(error)){ | ||
| stop('Error is not numeric') | ||
| } | ||
| if(!all(polarity %in% c('pos', 'neg'))){ | ||
| stop('Polarity is not pos and/or neg') | ||
| } | ||
| if(ion_type != 'ESI' & ion_type != 'MALDI'){ | ||
| stop('Ion_type is not ESI or MALDI') | ||
| } | ||
| if(!'mz' %in% names(ms2spectra)){ | ||
| stop('no mz column in ms2spectra') | ||
| } | ||
| if(!'precursorAnnotations' %in% names(ms2spectra)){ | ||
| stop('no precursorAnnotations column in ms2spectra') | ||
| } | ||
| if(!any(precursorAnnotations %in% ms2spectra$precursorAnnotations)){ | ||
| stop('none of the precursorAnnotations are in the precursorAnnotations', | ||
| 'column of the ms2spectra dataframe') | ||
| } | ||
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| #use default sep if none provided | ||
| if(is.null(precursorAnnotations_sep)){ | ||
| precursorAnnotations_sep = ':' | ||
| } | ||
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| #make an empty list | ||
| ms2_annot_list <- list() | ||
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| #fill in list with dfs for annotated spectra, with one entry per annotation | ||
| for(i in 1:length(precursorAnnotations)){ | ||
| #get annotation | ||
| annot = precursorAnnotations[i] | ||
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| #get dp from annotation | ||
| if (grepl(',', annot)){ | ||
| #if multiple annotations, get maximum dp | ||
| annots <- stringr::str_split_1(annot, ',') | ||
| dps <- stringr::str_split_i(annots, | ||
| precursorAnnotations_sep, | ||
| 3) %>% as.numeric() | ||
| max_dp = max(dps) | ||
| } else { | ||
| #otherwise just get the dp | ||
| max_dp = stringr::str_split_i(annot, | ||
| precursorAnnotations_sep, | ||
| 3) %>% as.numeric() | ||
| } | ||
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| #get modifications from annotations | ||
| #split by separator or space | ||
| p = paste0(' |', precursorAnnotations_sep) | ||
| annot_split <- stringr::str_split_1(annot, pattern = p) | ||
| #remove elements with the ion | ||
| annot_split <- annot_split[!grepl('\\[', annot_split)] %>% | ||
| #remove numbers | ||
| gsub('\\d', '', .) %>% | ||
| #make unique | ||
| unique() | ||
| #remove hexose (always included) | ||
| #only keep elements with word characters | ||
| annot_split <- annot_split[annot_split != 'Hex' & | ||
| grepl('\\w',annot_split)] | ||
| #if no modifications, set to 'none' | ||
| if(length(annot_split) == 0){ | ||
| annot_split <- 'none' | ||
| } | ||
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| #make sure everything is lower case | ||
| annot_split_lc <- stringr::str_to_lower(annot_split) %>% | ||
| sub('-', '', .) | ||
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| #get pentose option | ||
| if(any(annot_split == 'pen')){ | ||
| pent_option = T | ||
| } else { | ||
| pent_option = F | ||
| } | ||
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| #create parameter object | ||
| gpp <- GlycoAnnotateR::glycoPredictParam(dp = c(1, max_dp), | ||
| pent_option = pent_option, | ||
| modifications = annot_split_lc, | ||
| polarity = polarity, | ||
| scan_range = c(0, 10000), #set the scan range wide | ||
| ion_type = ion_type, | ||
| nmod_max = nmod_max, | ||
| double_sulfate = double_sulfate, | ||
| label = label) | ||
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| #make df for annotation | ||
| df <- ms2spectra %>% | ||
| #filter for precursor annotation | ||
| dplyr::filter(precursorAnnotations == !!annot) | ||
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| #annotate fragments | ||
| df_annot <- GlycoAnnotateR::glycoAnnotate(df, | ||
| param = gpp, | ||
| collapse = T, | ||
| error = error, | ||
| error_units = error_units) | ||
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| #add to list | ||
| ms2_annot_list[[i]] <- df_annot | ||
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| } | ||
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| #bind dfs in list into one df | ||
| ms2spectra_annotated <- ms2_annot_list %>% | ||
| dplyr::bind_rows() | ||
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| #return output | ||
| return(ms2spectra_annotated) | ||
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| } | ||
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