Commit ⋅ rformassspectrometry/MetaboCoreUtils

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R/chemFormula.R changed.

54.55% 92.86% +14.55%

R/zzz.R changed.

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DESCRIPTION has changed.

tests/testthat/test_chemFormula.R has changed.

NEWS.md has changed.

tests/testthat/test_zzz.R has changed.

man/calculateMass.Rd has changed.

@@ -23,25 +23,30 @@

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23	23		## regex pattern to isolate all elements
24	24		element_pattern <- paste0(
25	25		"(?<Element>",
26		-	"[A][cglmrstu]\|",
27		-	"[B][aehikr]?\|",
28		-	"[C][adeflmnorsu]?\|",
29		-	"[D][bsy]\|",
30		-	"[E][rsu]\|",
31		-	"[F][elmr]?\|",
32		-	"[G][ade]\|",
33		-	"[H][efgos]?\|",
34		-	"[I][nr]?\|",
35		-	"[K][r]?\|",
36		-	"[L][airuv]\|",
37		-	"[M][cdgnot]\|",
38		-	"[N][abdehiop]?\|",
39		-	"[O][gs]?\|",
40		-	"[P][abdmortu]?\|",
41		-	"[R][abefghnu]\|",
42		-	"[S][bcegimnr]?\|",
43		-	"[T][abcehilms]\|",
44		-	"[U]\|[V]\|[W]\|[X][e]\|[Y][b]?\|[Z][nr]",
	26	+	paste0("[0-9]*",
	27	+	c(
	28	+	"[A][cglmrstu]\|",
	29	+	"[B][aehikr]?\|",
	30	+	"[C][adeflmnorsu]?\|",
	31	+	"[D][bsy]\|",
	32	+	"[E][rsu]\|",
	33	+	"[F][elmr]?\|",
	34	+	"[G][ade]\|",
	35	+	"[H][efgos]?\|",
	36	+	"[I][nr]?\|",
	37	+	"[K][r]?\|",
	38	+	"[L][airuv]\|",
	39	+	"[M][cdgnot]\|",
	40	+	"[N][abdehiop]?\|",
	41	+	"[O][gs]?\|",
	42	+	"[P][abdmortu]?\|",
	43	+	"[R][abefghnu]\|",
	44	+	"[S][bcegimnr]?\|",
	45	+	"[T][abcehilms]\|",
	46	+	"[U]\|[V]\|[W]\|[X][e]\|[Y][b]?\|[Z][nr]"
	47	+	),
	48	+	collapse = ""
	49	+	),
45	50		")",
46	51		"(?<Number>[0-9]*)"
47	52		)

@@ -56,10 +61,30 @@

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        sbstr[!nchar(sbstr)] <- 1L
        sl <- seq_len(n)
        nm <- sbstr[sl]
        setNames(as.integer(sbstr[n + sl]), nm)
        r <- setNames(as.integer(sbstr[n + sl]), nm)
        valid <- .isValidElementName(nm)

        if (any(!valid)) {
            warning(
                "The following names are not valid and are dropped: ",
                paste0(names(r)[!valid], collapse = ", ")
            )
            r <- r[valid]
        }
        r
    }, xx = x, rr = rx, SIMPLIFY = FALSE, USE.NAMES = TRUE)
}

#' Validate element names/heavy isotopes
#'
#' @param x `character`, element/heavy isotope names
#' @return `logical`, `TRUE` for valid name, `FALSE` otherwise
#'
#' @noRd
.isValidElementName <- function(x) {
    x %in% names(.ISOTOPES)
}

#' @title Create chemical formula from a named vector
#'
#' @description

@@ -92,7 +117,10 @@

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    enms <- .sort_elements(names(x))
    y <- as.character(x[enms])
    y[y == "1"] <- ""
    paste0(enms, y, collapse = "")
    y <- paste0(enms, y)
    ## brackets for heavy isotopes
    y <- gsub("^([0-9]+[A-z]+[0-9]*)", "[\\1]", y)
    paste0(y, collapse = "")
}

#' Sort elements starting with organic elements, according to the Hill notation

@@ -105,9 +133,7 @@

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105	133		#' @examples
106	134		#' .sort_elements(c("H", "O", "S", "P", "C", "N", "Na", "Fe"))
107	135		.sort_elements <- function(x) {
108		-	org <- c("C", "H", "N", "O", "S", "P")
109		-	y <- c(org, sort(x[!x %in% org]))
110		-	x[match(y, x, nomatch = 0L)]
	136	+	x[match(names(.ISOTOPES), x, nomatch = 0L)]
111	137		}
112	138
113	139		#' @title Standardize a chemical formula

@@ -260,18 +286,19 @@

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#' calculateMass("C6H12O6")
#' calculateMass("NH3")
#' calculateMass(c("C6H12O6", "NH3"))
#' calculateMass(c("C6H12O6", "[13C3]C3H12O6"))
calculateMass <- function(x) {
    if (is.character(x))
        x <- countElements(x)
    if (!is.list(x))
        stop("x must be either a character or a list with element counts.")
    vapply(x, function(z) {
        elements <- names(z)
        if (!all(elements %in% names(.MONOISOTOPES))) {
            message("not for all elements a monoisotopic mass is found")
        isotopes <- names(z)
        if (!length(z) || !all(isotopes %in% names(.ISOTOPES))) {
            message("not for all isotopes a mass is found")
            return(NA_real_)
        }
        sum(z * .MONOISOTOPES[elements])
        sum(z * .ISOTOPES[isotopes])
        ## mass <- 0.0
        ## for (atom in elements) {
        ##     atom_mass <- .MONOISOTOPES[atom]

@@ -17,7 +17,7 @@

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    }

    # get mono isotopes for exact mass calculation
    assign(".MONOISOTOPES", .load_isotopes(), envir = asNamespace(pkgname))
    assign(".ISOTOPES", .load_isotopes(), envir = asNamespace(pkgname))
}

.load_adducts <- function() {

@@ -29,9 +29,24 @@

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}

.load_isotopes <- function() {
    mono <- utils::read.table(system.file("isotopes", "isotope_definition.txt",
                                          package = "MetaboCoreUtils"),
                              sep = "\t", header = TRUE)
    vapply(split(mono, mono$element), function(z)
        z$exact_mass[which.max(z$rel_abundance)], numeric(1))
    iso <- utils::read.table(
        system.file(
            "isotopes", "isotope_definition.txt", package = "MetaboCoreUtils"
        ),
        sep = "\t", header = TRUE
    )
    ## sort by rel_abundance
    iso <- iso[order(iso$element, -iso$rel_abundance),]
    ## swap numbers and elements names
    iso$isotope <- gsub("([A-z]+)([0-9]*)", "\\2\\1", iso$isotope)
    ## drop isotope number from most common isotope
    is_most_common <- !duplicated(iso$element)
    iso$isotope[is_most_common] <-
        gsub("^[0-9]+", "", iso$isotope[is_most_common])
    ## sort according to Hill notation
    org <- c("C", "H", "N", "O", "S", "P")
    iso$rank <- match(iso$element, org, nomatch = length(org) + 1L)
    ## reorder according to Hill notation and non-common isotopes first
    iso <- iso[order(iso$rank, iso$element, iso$isotope),]
    setNames(iso$exact_mass, iso$isotope)
}

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R	348	319	0	29	91.67%
Project Totals (8 files)	348	319	0	29	91.67%

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56	61		sbstr[!nchar(sbstr)] <- 1L
57	62		sl <- seq_len(n)
58	63		nm <- sbstr[sl]
59		-	setNames(as.integer(sbstr[n + sl]), nm)
	64	+	r <- setNames(as.integer(sbstr[n + sl]), nm)
	65	+	valid <- .isValidElementName(nm)
	66	+
	67	+	if (any(!valid)) {
	68	+	warning(
	69	+	"The following names are not valid and are dropped: ",
	70	+	paste0(names(r)[!valid], collapse = ", ")
	71	+	)
	72	+	r <- r[valid]
	73	+	}
	74	+	r
60	75		}, xx = x, rr = rx, SIMPLIFY = FALSE, USE.NAMES = TRUE)
61	76		}
62	77
	78	+	#' Validate element names/heavy isotopes
	79	+	#'
	80	+	#' @param x `character`, element/heavy isotope names
	81	+	#' @return `logical`, `TRUE` for valid name, `FALSE` otherwise
	82	+	#'
	83	+	#' @noRd
	84	+	.isValidElementName <- function(x) {
	85	+	x %in% names(.ISOTOPES)
	86	+	}
	87	+
63	88		#' @title Create chemical formula from a named vector
64	89		#'
65	90		#' @description

92	117		enms <- .sort_elements(names(x))
93	118		y <- as.character(x[enms])
94	119		y[y == "1"] <- ""
95		-	paste0(enms, y, collapse = "")
	120	+	y <- paste0(enms, y)
	121	+	## brackets for heavy isotopes
	122	+	y <- gsub("^([0-9]+[A-z]+[0-9]*)", "[\\1]", y)
	123	+	paste0(y, collapse = "")
96	124		}
97	125
98	126		#' Sort elements starting with organic elements, according to the Hill notation

260	286		#' calculateMass("C6H12O6")
261	287		#' calculateMass("NH3")
262	288		#' calculateMass(c("C6H12O6", "NH3"))
	289	+	#' calculateMass(c("C6H12O6", "[13C3]C3H12O6"))
263	290		calculateMass <- function(x) {
264	291		if (is.character(x))
265	292		x <- countElements(x)
266	293		if (!is.list(x))
267	294		stop("x must be either a character or a list with element counts.")
268	295		vapply(x, function(z) {
269		-	elements <- names(z)
270		-	if (!all(elements %in% names(.MONOISOTOPES))) {
271		-	message("not for all elements a monoisotopic mass is found")
	296	+	isotopes <- names(z)
	297	+	if (!length(z) \|\| !all(isotopes %in% names(.ISOTOPES))) {
	298	+	message("not for all isotopes a mass is found")
272	299		return(NA_real_)
273	300		}
274		-	sum(z * .MONOISOTOPES[elements])
	301	+	sum(z * .ISOTOPES[isotopes])
275	302		## mass <- 0.0
276	303		## for (atom in elements) {
277	304		## atom_mass <- .MONOISOTOPES[atom]

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17	17		}
18	18
19	19		# get mono isotopes for exact mass calculation
20		-	assign(".MONOISOTOPES", .load_isotopes(), envir = asNamespace(pkgname))
	20	+	assign(".ISOTOPES", .load_isotopes(), envir = asNamespace(pkgname))
21	21		}
22	22
23	23		.load_adducts <- function() {

29	29		}
30	30
31	31		.load_isotopes <- function() {
32		-	mono <- utils::read.table(system.file("isotopes", "isotope_definition.txt",
33		-	package = "MetaboCoreUtils"),
34		-	sep = "\t", header = TRUE)
35		-	vapply(split(mono, mono$element), function(z)
36		-	z$exact_mass[which.max(z$rel_abundance)], numeric(1))
	32	+	iso <- utils::read.table(
	33	+	system.file(
	34	+	"isotopes", "isotope_definition.txt", package = "MetaboCoreUtils"
	35	+	),
	36	+	sep = "\t", header = TRUE
	37	+	)
	38	+	## sort by rel_abundance
	39	+	iso <- iso[order(iso$element, -iso$rel_abundance),]
	40	+	## swap numbers and elements names
	41	+	iso$isotope <- gsub("([A-z]+)([0-9]*)", "\\2\\1", iso$isotope)
	42	+	## drop isotope number from most common isotope
	43	+	is_most_common <- !duplicated(iso$element)
	44	+	iso$isotope[is_most_common] <-
	45	+	gsub("^[0-9]+", "", iso$isotope[is_most_common])
	46	+	## sort according to Hill notation
	47	+	org <- c("C", "H", "N", "O", "S", "P")
	48	+	iso$rank <- match(iso$element, org, nomatch = length(org) + 1L)
	49	+	## reorder according to Hill notation and non-common isotopes first
	50	+	iso <- iso[order(iso$rank, iso$element, iso$isotope),]
	51	+	setNames(iso$exact_mass, iso$isotope)
37	52		}

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