R/parser.R
In cole-trapnell-lab/garnett: Automated cell type classification
Lexer <- R6::R6Class(
"Lexer",
public = list(
tokens = c("KEYWORD", "NAME", "NEWLINE", "NUM",
"SIMP_KEY", "COM"),
literals = c(">", ":", ","),
t_COM = function(re='#.*',t) {}, # Comment character
t_KEYWORD =
c('expressed below|expressed above|expressed between|subtype of'),
t_SIMP_KEY = c('celltype|expressed|not expressed|references'),
t_NAME =
'[a-zA-Z0-9_+/\\-\\.|=`~\\*&<^%?@!$();:]*[a-zA-Z][a-zA-Z0-9_+/\\-\\.|=`~\\*&<^%?@!$();]*',
t_NUM = '([0-9]*\\.[0-9]+)|([0-9]+)',
t_ignore = " \t",
t_NEWLINE = "\n|\r\n",
t_error = function(t) {
cat(sprintf(" Marker file error. Illegal character '%s'\n", t$value[1]))
t$lexer$skip(1)
return(t)
}
)
)
#' Parsing the Garnett marker file
#'
#' Garnett uses a marker file to allow users to specify cell type definitions.
#' While the marker file is designed to be easy to construct and human-readable,
#' it is parsed by Garnett automatically, and so it needs to follow certain
#' formatting constraints.
#'
#' The following describes the constraints necessary in the input to the
#' \code{marker_file} argument of \code{\link{train_cell_classifier}} and
#' \code{\link{check_markers}}.
#'
#' @section Elements of a cell type description:
#' The basic structure of the Garnett marker file is a series of entries, each
#' describing elements of a cell type. After the cell name, each additional
#' line will be a descriptor, which begins with a keyword, followed by a colon
#' (':'). After the colon, a series of specifications can be added, separated
#' by commas (','). Descriptors may spill onto following lines so long as you
#' do not split a specification across multiple lines (i.e. if breaking up a
#' long descriptor across multiple lines, all but the last line should end with
#' a comma). Each new descriptor should begin on a new line. A generic cell
#' type entry looks like this:
#'
#' ```
#' > cell type name
#' descriptor: spec1, spec2,
#' spec3, spec4
#' descriptor2: spec1
#' ```
#'
#' The following are the potential descriptors:
#' \describe{
#' \item{cell name}{\strong{Required} Each cell type must have a unique name,
#' and the name should head the cell type description. To indicate a new cell
#' type, use the \code{>} symbol, followed by the cell name, followed by a
#' new line. For example, \code{> T cell}.}
#' \item{expressed:}{\strong{Required} After the cell name, the minimal
#' requirement for each cell type is the name of a single marker gene. The
#' line in the marker file will begin with \code{expressed:}, followed by one
#' or more gene names separated by commas. The last gene name of the
#' descriptor is not followed by a comma. Gene IDs can be of any type
#' (ENSEMBL, SYMBOL, etc.) that is present in the Bioconductor
#' \code{\link[AnnotationDbi]{AnnotationDb-class}} package for your species.
#' (See available packages on the
#' \href{http://bioconductor.org/packages/3.8/data/annotation/}{Bioconductor website}).
#' For example, for human, use \code{\link[org.Hs.eg.db]{org.Hs.eg.db}}. To
#' see available gene ID types, you can run \code{columns(db)}. You will
#' specify which gene ID type you used when calling
#' \code{\link{train_cell_classifier}}.} If your species does not have an
#' annotation dataset of type \code{\link[AnnotationDbi]{AnnotationDb-class}},
#' you can set \code{db = 'none'}, however Garnett will then not convert gene
#' ID types, so CDS and marker file gene ID types need to be the same.
#' \item{not expressed:}{In addition to
#' specifying genes that the cell type should express, you can also specify
#' genes that your cell type should not express. Details on specifying genes
#' are the same as for \code{expressed:}.}
#' \item{subtype of:}{When present, this descriptor specifies that a cell
#' type is a subtype of another cell type that is also described in the
#' marker file. A biological example would be a CD4 T cell being a subtype of
#' a T cell. This descriptor causes the cell type to be classified on a
#' separate sub-level of the classification hierarchy, after the
#' classification of its parent type is done (i.e. first T cells are
#' discriminated from other cell types, then the T cells are subclassified
#' using any cell types with the descriptor \code{subtype of: T cell}).
#' \code{subtype of:} can only include a single specification, and the
#' specification must be the exact name of another cell type specified in
#' this marker file.}
#' \item{references:}{This descriptor is not required, but is highly
#' recommended. The specifications for this descriptor should be links/DOIs
#' documenting how you chose your marker genes. While these specifications
#' will not influence cell type classification, they will be packaged with
#' the built classifier so that future users of the classifier can trace the
#' origins of the markers/ }
#' \item{*meta data:}{This wildcard descriptor allows you to specify any
#' other property of a cell type that you wish to specify. The keyword will
#' be the name of the column in your \code{pData} (meta data) table that you
#' wish to specify, and the specifications will be a list of acceptable
#' values for that meta data. An example use of this would be
#' \code{tissue: liver, kidney}, which would specify that training cells for
#' this cell type must have "liver" or "kidney" as their entry in the
#' "tissue" column of the \code{pData} table.}
#' \item{expressed below:}{While we recommend that you use \code{expressed:}
#' and \code{not expressed:} to specify the cell type's marker genes, because
#' these terms utilize the entirety of Garnett's built-in normalization and
#' standardization, you can also specify expression using the following
#' logical descriptors
#' \code{expressed below:, expressed above:, expressed between:}.
#' Note that no normalization occurs with these descriptors; they are used as
#' logical gates only. To specify \code{expressed below:}, use the gene name,
#' followed by a space, followed by a number. This will only allow training
#' cells that have this gene expressed below the given value \strong{in the
#' units of the expression matrix provided}. For example,
#' \code{expressed below: MYOD1 7, MYH3 2}.}
#' \item{expressed above:}{Similar to \code{expressed below:}, but will only
#' allow training cells expressing the given gene above the value provided.}
#' \item{expressed between:}{Similar to \code{expressed below:}, but provide
#' two values separated by spaces. For example
#' \code{expressed between: ACT5 2 5.5, ACT2 1 2.7}. This descriptor will
#' only allow training cells expressing the given gene between the two values
#' provided.}
#' }
#' @section Checking your marker file:
#'
#' Because only specific expressed markers are useful for Garnett
#' classification, we recommend that you always check your marker file for
#' ambiguity before proceeding with classification. To do this, we have
#' provided the functions \code{\link{check_markers}} and
#' \code{\link{plot_markers}} to facilitate marker checking. See that manual
#' pages for those functions for details.
#'
#' @seealso \code{\link{train_cell_classifier}}
#'
Parser <- R6::R6Class(
"Parser",
public = list(
tokens = c("KEYWORD", "NAME", "NEWLINE",
"SIMP_KEY", "NUM"),
literals = c(">", ":", ","),
# Parsing rules
linenum = 1,
p_file_1 = function(doc="file : NEWLINE file", p) {
p$set(1, p$get(3))
},
p_file_2 = function(doc="file : celltype
| file celltype", p) {
if(p$length() == 2) {
cts = new.env(hash=TRUE)
name_order <- list()
cts[["name_order"]] <- name_order
cell_ont <- p$get(2)
cts[[cell_ont@name]] <- cell_ont
cts[["name_order"]] <- c(cts[["name_order"]], cell_ont@name)
} else {
cts <- p$get(2)
cell_ont <- p$get(3)
if(cell_ont@name %in% names(cts)) {
stop(paste0("Cell type '", cell_ont@name,
"' is defined a second time at or near line ",
self[["linenum"]], "."))
}
cts[[cell_ont@name]] <- cell_ont
cts[["name_order"]] <- c(cts[["name_order"]], cell_ont@name)
}
p$set(1, cts)
},
p_header_start = function(doc="header_start : '>' NAME
| '>' NUM
| header_start NUM
| header_start NAME", p) {
if (is.character(p$get(2))) {
ct <- new("cell_rules")
ct@name <- p$get(3)
} else {
ct <- p$get(2)
ct@name <- paste(ct@name, p$get(3))
}
p$set(1, ct)
},
p_header_1 = function(doc="header : header_start NEWLINE", p) {
self[["linenum"]] <- self[["linenum"]] + 1
p$set(1, p$get(2))
},
p_celltype_1 = function(doc="celltype : header", p) {
p$set(1, p$get(2))
},
p_celltype_2 = function(doc="celltype : celltype rule", p) {
ct <- p$get(2)
rule <- p$get(3)
if (rule[[1]] == "exp") {
ct@expressed <- c(ct@expressed, rule[2:length(rule)])
} else if (rule[[1]] == "nexp") {
ct@not_expressed <- c(ct@not_expressed, rule[2:length(rule)])
} else if (rule[[1]] == "ref") {
ct@references <- c(ct@references, rule[2:length(rule)])
} else if (rule[[1]] == "sub") {
ct@parenttype <- rule[[2]]
} else if (rule[[1]] == "meta") {
if (nrow(ct@meta) == 0) {
ct@meta <- rule[[2]]
} else {
ct@meta <- rbind(ct@meta, rule[[2]])
}
} else if (rule[[1]] %in% c("exp_ab", "exp_bel", "exp_bet")) {
ct@gene_rules <- c(ct@gene_rules, rule[2:length(rule)])
}
p$set(1, ct)
},
p_rule_head_1 = function(doc="rule_head : SIMP_KEY ':'", p) {
p$set(1, p$get(2))
},
p_rule_head_comp_1 = function(doc="rule_head_comp : KEYWORD ':'", p) {
p$set(1, p$get(2))
},
p_rule_head_2 = function(doc="rule_head : NAME ':'", p) {
p$set(1, p$get(2))
},
p_rule_1 = function(doc="rule : rule_head expression NEWLINE", p) {
self[["linenum"]] <- self[["linenum"]] + 1
if(p$get(2) == "expressed") {
p$set(1, c("exp", p$get(3)))
} else if(p$get(2) == "not expressed") {
p$set(1, c("nexp", p$get(3)))
} else if(p$get(2) == "references") {
p$set(1, c("ref", p$get(3)))
} else {
p$set(1, list("meta", data.frame(name = p$get(2),
spec = p$get(3),
stringsAsFactors = FALSE)))
}
},
p_rule_2 = function(doc="rule : rule_head_comp comp_expression NEWLINE",
p) {
self[["linenum"]] <- self[["linenum"]] + 1
if(!is.list(p$get(3))) p$set(3, list(p$get(3)))
if(p$get(2) == "expressed above") {
grs <- lapply(p$get(3), function(x) {
if (length(x) != 2) stop(paste0("Syntax error in marker file at or",
" near line ", self[["linenum"]],
": expressed above needs one ",
"value"))
x <- new("gene_rule", gene_name = x[1],
lower = as.numeric(x[2]), upper = Inf)
})
p$set(1, c("exp_ab", grs))
} else if(p$get(2) == "expressed below") {
grs <- lapply(p$get(3), function(x) {
if (length(x) != 2) stop(paste0("Syntax error in marker file at or",
" near line ", self[["linenum"]],
": expressed below needs one ",
"value"))
x <- new("gene_rule", gene_name = x[1], upper = as.numeric(x[2]),
lower = -1)
})
p$set(1, c("exp_bel", grs))
} else if(p$get(2) == "expressed between") {
grs <- lapply(p$get(3), function(x) {
if (length(x) != 3) stop(paste0("Syntax error in marker file at or",
" near line ", self[["linenum"]],
": expressed between needs two",
" values"))
n1 <- as.numeric(x[2])
n2 <- as.numeric(x[3])
if (n1 > n2) stop(paste0("expressed between: ", x[1],
" has expression values out of order ",
"- swapping."))
x <- new("gene_rule", gene_name = x[1], lower = min(n1, n2),
upper = max(n1, n2))
})
p$set(1, c("exp_bet", grs))
} else if(p$get(2) == "subtype of") {
p$set(1, list("sub", paste(unlist(p$get(3)), collapse = " ")))
}
},
p_rule_3 = function(doc="rule : rule NEWLINE", p) {
p$set(1, p$get(2))
self[["linenum"]] <- self[["linenum"]] + 1
},
p_expression_1 = function(doc="expression : NAME
| NUM", p) {
p$set(1, p$get(2))
},
p_expression_2 = function(doc="expression : expression NAME
| expression NUM", p) {
if(length(p$get(2)) == 1) {
p$set(1, paste(p$get(2), p$get(3)))
} else {
p$set(1, c(p$get(2)[1:(length(p$get(2)) - 1)],
paste(p$get(2)[length(p$get(2))], p$get(3))))
}
},
p_expression_3 = function(doc="expression : expression ',' NAME
| expression ',' NUM", p) {
p$set(1, c(p$get(2), p$get(4)))
},
p_expression_4 = function(doc="expression : expression ',' NEWLINE NAME
| expression ',' NEWLINE NUM",
p) {
p$set(1, c(p$get(2), p$get(5)))
},
p_comp_expression_1 = function(doc="comp_expression : NAME
| NUM" , p) {
p$set(1, p$get(2))
},
p_comp_expression_2 = function(doc="comp_expression : comp_expression NUM
| comp_expression NAME",
p) {
p$set(1, c(p$get(2), p$get(3)))
},
p_comp_expression_3 =
function(doc="comp_expression : comp_expression ',' NAME NUM", p) {
l <- p$get(2)
if(!is.list(l)) l <- list(l)
l[[length(l) + 1]] <- c(p$get(4), p$get(5))
p$set(1, l)
},
p_comp_expression_4 =
function(doc="comp_expression : comp_expression ',' NEWLINE NAME NUM",
p) {
l <- p$get(2)
if(!is.list(l)) l <- list(l)
l[[length(l) + 1]] <- c(p$get(5), p$get(6))
p$set(1, l)
},
p_comp_expression_5 =
function(doc="comp_expression : comp_expression ',' NAME NUM NUM", p) {
l <- p$get(2)
if(!is.list(l)) l <- list(l)
l[[length(l) + 1]] <- c(p$get(4), p$get(5), p$get(6))
p$set(1, l)
},
p_comp_expression_6 =
function(doc="comp_expression : comp_expression ',' NEWLINE NAME NUM NUM",
p) {
l <- p$get(2)
if(!is.list(l)) l <- list(l)
l[[length(l) + 1]] <- c(p$get(5), p$get(6), p$get(7))
p$set(1, l)
},
p_error = function(p) {
if(is.null(p)) stop("Marker file error. Syntax error at EOF")
else stop(sprintf("Marker file error. Syntax error '%s' at or near line number %s\n",
p$value, self[["linenum"]]))
}
)
)
cole-trapnell-lab/garnett documentation built on Jan. 6, 2025, 2:18 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Lexer <- R6::R6Class(
"Lexer",
public = list(
tokens = c("KEYWORD", "NAME", "NEWLINE", "NUM",
"SIMP_KEY", "COM"),
literals = c(">", ":", ","),
t_COM = function(re='#.*',t) {}, # Comment character
t_KEYWORD =
c('expressed below|expressed above|expressed between|subtype of'),
t_SIMP_KEY = c('celltype|expressed|not expressed|references'),
t_NAME =
'[a-zA-Z0-9_+/\\-\\.|=`~\\*&<^%?@!$();:]*[a-zA-Z][a-zA-Z0-9_+/\\-\\.|=`~\\*&<^%?@!$();]*',
t_NUM = '([0-9]*\\.[0-9]+)|([0-9]+)',
t_ignore = " \t",
t_NEWLINE = "\n|\r\n",
t_error = function(t) {
cat(sprintf(" Marker file error. Illegal character '%s'\n", t$value[1]))
t$lexer$skip(1)
return(t)
}
)
)
#' Parsing the Garnett marker file
#'
#' Garnett uses a marker file to allow users to specify cell type definitions.
#' While the marker file is designed to be easy to construct and human-readable,
#' it is parsed by Garnett automatically, and so it needs to follow certain
#' formatting constraints.
#'
#' The following describes the constraints necessary in the input to the
#' \code{marker_file} argument of \code{\link{train_cell_classifier}} and
#' \code{\link{check_markers}}.
#'
#' @section Elements of a cell type description:
#' The basic structure of the Garnett marker file is a series of entries, each
#' describing elements of a cell type. After the cell name, each additional
#' line will be a descriptor, which begins with a keyword, followed by a colon
#' (':'). After the colon, a series of specifications can be added, separated
#' by commas (','). Descriptors may spill onto following lines so long as you
#' do not split a specification across multiple lines (i.e. if breaking up a
#' long descriptor across multiple lines, all but the last line should end with
#' a comma). Each new descriptor should begin on a new line. A generic cell
#' type entry looks like this:
#'
#' ```
#' > cell type name
#' descriptor: spec1, spec2,
#' spec3, spec4
#' descriptor2: spec1
#' ```
#'
#' The following are the potential descriptors:
#' \describe{
#' \item{cell name}{\strong{Required} Each cell type must have a unique name,
#' and the name should head the cell type description. To indicate a new cell
#' type, use the \code{>} symbol, followed by the cell name, followed by a
#' new line. For example, \code{> T cell}.}
#' \item{expressed:}{\strong{Required} After the cell name, the minimal
#' requirement for each cell type is the name of a single marker gene. The
#' line in the marker file will begin with \code{expressed:}, followed by one
#' or more gene names separated by commas. The last gene name of the
#' descriptor is not followed by a comma. Gene IDs can be of any type
#' (ENSEMBL, SYMBOL, etc.) that is present in the Bioconductor
#' \code{\link[AnnotationDbi]{AnnotationDb-class}} package for your species.
#' (See available packages on the
#' \href{http://bioconductor.org/packages/3.8/data/annotation/}{Bioconductor website}).
#' For example, for human, use \code{\link[org.Hs.eg.db]{org.Hs.eg.db}}. To
#' see available gene ID types, you can run \code{columns(db)}. You will
#' specify which gene ID type you used when calling
#' \code{\link{train_cell_classifier}}.} If your species does not have an
#' annotation dataset of type \code{\link[AnnotationDbi]{AnnotationDb-class}},
#' you can set \code{db = 'none'}, however Garnett will then not convert gene
#' ID types, so CDS and marker file gene ID types need to be the same.
#' \item{not expressed:}{In addition to
#' specifying genes that the cell type should express, you can also specify
#' genes that your cell type should not express. Details on specifying genes
#' are the same as for \code{expressed:}.}
#' \item{subtype of:}{When present, this descriptor specifies that a cell
#' type is a subtype of another cell type that is also described in the
#' marker file. A biological example would be a CD4 T cell being a subtype of
#' a T cell. This descriptor causes the cell type to be classified on a
#' separate sub-level of the classification hierarchy, after the
#' classification of its parent type is done (i.e. first T cells are
#' discriminated from other cell types, then the T cells are subclassified
#' using any cell types with the descriptor \code{subtype of: T cell}).
#' \code{subtype of:} can only include a single specification, and the
#' specification must be the exact name of another cell type specified in
#' this marker file.}
#' \item{references:}{This descriptor is not required, but is highly
#' recommended. The specifications for this descriptor should be links/DOIs
#' documenting how you chose your marker genes. While these specifications
#' will not influence cell type classification, they will be packaged with
#' the built classifier so that future users of the classifier can trace the
#' origins of the markers/ }
#' \item{*meta data:}{This wildcard descriptor allows you to specify any
#' other property of a cell type that you wish to specify. The keyword will
#' be the name of the column in your \code{pData} (meta data) table that you
#' wish to specify, and the specifications will be a list of acceptable
#' values for that meta data. An example use of this would be
#' \code{tissue: liver, kidney}, which would specify that training cells for
#' this cell type must have "liver" or "kidney" as their entry in the
#' "tissue" column of the \code{pData} table.}
#' \item{expressed below:}{While we recommend that you use \code{expressed:}
#' and \code{not expressed:} to specify the cell type's marker genes, because
#' these terms utilize the entirety of Garnett's built-in normalization and
#' standardization, you can also specify expression using the following
#' logical descriptors
#' \code{expressed below:, expressed above:, expressed between:}.
#' Note that no normalization occurs with these descriptors; they are used as
#' logical gates only. To specify \code{expressed below:}, use the gene name,
#' followed by a space, followed by a number. This will only allow training
#' cells that have this gene expressed below the given value \strong{in the
#' units of the expression matrix provided}. For example,
#' \code{expressed below: MYOD1 7, MYH3 2}.}
#' \item{expressed above:}{Similar to \code{expressed below:}, but will only
#' allow training cells expressing the given gene above the value provided.}
#' \item{expressed between:}{Similar to \code{expressed below:}, but provide
#' two values separated by spaces. For example
#' \code{expressed between: ACT5 2 5.5, ACT2 1 2.7}. This descriptor will
#' only allow training cells expressing the given gene between the two values
#' provided.}
#' }
#' @section Checking your marker file:
#'
#' Because only specific expressed markers are useful for Garnett
#' classification, we recommend that you always check your marker file for
#' ambiguity before proceeding with classification. To do this, we have
#' provided the functions \code{\link{check_markers}} and
#' \code{\link{plot_markers}} to facilitate marker checking. See that manual
#' pages for those functions for details.
#'
#' @seealso \code{\link{train_cell_classifier}}
#'
Parser <- R6::R6Class(
"Parser",
public = list(
tokens = c("KEYWORD", "NAME", "NEWLINE",
"SIMP_KEY", "NUM"),
literals = c(">", ":", ","),
# Parsing rules
linenum = 1,
p_file_1 = function(doc="file : NEWLINE file", p) {
p$set(1, p$get(3))
},
p_file_2 = function(doc="file : celltype
| file celltype", p) {
if(p$length() == 2) {
cts = new.env(hash=TRUE)
name_order <- list()
cts[["name_order"]] <- name_order
cell_ont <- p$get(2)
cts[[cell_ont@name]] <- cell_ont
cts[["name_order"]] <- c(cts[["name_order"]], cell_ont@name)
} else {
cts <- p$get(2)
cell_ont <- p$get(3)
if(cell_ont@name %in% names(cts)) {
stop(paste0("Cell type '", cell_ont@name,
"' is defined a second time at or near line ",
self[["linenum"]], "."))
}
cts[[cell_ont@name]] <- cell_ont
cts[["name_order"]] <- c(cts[["name_order"]], cell_ont@name)
}
p$set(1, cts)
},
p_header_start = function(doc="header_start : '>' NAME
| '>' NUM
| header_start NUM
| header_start NAME", p) {
if (is.character(p$get(2))) {
ct <- new("cell_rules")
ct@name <- p$get(3)
} else {
ct <- p$get(2)
ct@name <- paste(ct@name, p$get(3))
}
p$set(1, ct)
},
p_header_1 = function(doc="header : header_start NEWLINE", p) {
self[["linenum"]] <- self[["linenum"]] + 1
p$set(1, p$get(2))
},
p_celltype_1 = function(doc="celltype : header", p) {
p$set(1, p$get(2))
},
p_celltype_2 = function(doc="celltype : celltype rule", p) {
ct <- p$get(2)
rule <- p$get(3)
if (rule[[1]] == "exp") {
ct@expressed <- c(ct@expressed, rule[2:length(rule)])
} else if (rule[[1]] == "nexp") {
ct@not_expressed <- c(ct@not_expressed, rule[2:length(rule)])
} else if (rule[[1]] == "ref") {
ct@references <- c(ct@references, rule[2:length(rule)])
} else if (rule[[1]] == "sub") {
ct@parenttype <- rule[[2]]
} else if (rule[[1]] == "meta") {
if (nrow(ct@meta) == 0) {
ct@meta <- rule[[2]]
} else {
ct@meta <- rbind(ct@meta, rule[[2]])
}
} else if (rule[[1]] %in% c("exp_ab", "exp_bel", "exp_bet")) {
ct@gene_rules <- c(ct@gene_rules, rule[2:length(rule)])
}
p$set(1, ct)
},
p_rule_head_1 = function(doc="rule_head : SIMP_KEY ':'", p) {
p$set(1, p$get(2))
},
p_rule_head_comp_1 = function(doc="rule_head_comp : KEYWORD ':'", p) {
p$set(1, p$get(2))
},
p_rule_head_2 = function(doc="rule_head : NAME ':'", p) {
p$set(1, p$get(2))
},
p_rule_1 = function(doc="rule : rule_head expression NEWLINE", p) {
self[["linenum"]] <- self[["linenum"]] + 1
if(p$get(2) == "expressed") {
p$set(1, c("exp", p$get(3)))
} else if(p$get(2) == "not expressed") {
p$set(1, c("nexp", p$get(3)))
} else if(p$get(2) == "references") {
p$set(1, c("ref", p$get(3)))
} else {
p$set(1, list("meta", data.frame(name = p$get(2),
spec = p$get(3),
stringsAsFactors = FALSE)))
}
},
p_rule_2 = function(doc="rule : rule_head_comp comp_expression NEWLINE",
p) {
self[["linenum"]] <- self[["linenum"]] + 1
if(!is.list(p$get(3))) p$set(3, list(p$get(3)))
if(p$get(2) == "expressed above") {
grs <- lapply(p$get(3), function(x) {
if (length(x) != 2) stop(paste0("Syntax error in marker file at or",
" near line ", self[["linenum"]],
": expressed above needs one ",
"value"))
x <- new("gene_rule", gene_name = x[1],
lower = as.numeric(x[2]), upper = Inf)
})
p$set(1, c("exp_ab", grs))
} else if(p$get(2) == "expressed below") {
grs <- lapply(p$get(3), function(x) {
if (length(x) != 2) stop(paste0("Syntax error in marker file at or",
" near line ", self[["linenum"]],
": expressed below needs one ",
"value"))
x <- new("gene_rule", gene_name = x[1], upper = as.numeric(x[2]),
lower = -1)
})
p$set(1, c("exp_bel", grs))
} else if(p$get(2) == "expressed between") {
grs <- lapply(p$get(3), function(x) {
if (length(x) != 3) stop(paste0("Syntax error in marker file at or",
" near line ", self[["linenum"]],
": expressed between needs two",
" values"))
n1 <- as.numeric(x[2])
n2 <- as.numeric(x[3])
if (n1 > n2) stop(paste0("expressed between: ", x[1],
" has expression values out of order ",
"- swapping."))
x <- new("gene_rule", gene_name = x[1], lower = min(n1, n2),
upper = max(n1, n2))
})
p$set(1, c("exp_bet", grs))
} else if(p$get(2) == "subtype of") {
p$set(1, list("sub", paste(unlist(p$get(3)), collapse = " ")))
}
},
p_rule_3 = function(doc="rule : rule NEWLINE", p) {
p$set(1, p$get(2))
self[["linenum"]] <- self[["linenum"]] + 1
},
p_expression_1 = function(doc="expression : NAME
| NUM", p) {
p$set(1, p$get(2))
},
p_expression_2 = function(doc="expression : expression NAME
| expression NUM", p) {
if(length(p$get(2)) == 1) {
p$set(1, paste(p$get(2), p$get(3)))
} else {
p$set(1, c(p$get(2)[1:(length(p$get(2)) - 1)],
paste(p$get(2)[length(p$get(2))], p$get(3))))
}
},
p_expression_3 = function(doc="expression : expression ',' NAME
| expression ',' NUM", p) {
p$set(1, c(p$get(2), p$get(4)))
},
p_expression_4 = function(doc="expression : expression ',' NEWLINE NAME
| expression ',' NEWLINE NUM",
p) {
p$set(1, c(p$get(2), p$get(5)))
},
p_comp_expression_1 = function(doc="comp_expression : NAME
| NUM" , p) {
p$set(1, p$get(2))
},
p_comp_expression_2 = function(doc="comp_expression : comp_expression NUM
| comp_expression NAME",
p) {
p$set(1, c(p$get(2), p$get(3)))
},
p_comp_expression_3 =
function(doc="comp_expression : comp_expression ',' NAME NUM", p) {
l <- p$get(2)
if(!is.list(l)) l <- list(l)
l[[length(l) + 1]] <- c(p$get(4), p$get(5))
p$set(1, l)
},
p_comp_expression_4 =
function(doc="comp_expression : comp_expression ',' NEWLINE NAME NUM",
p) {
l <- p$get(2)
if(!is.list(l)) l <- list(l)
l[[length(l) + 1]] <- c(p$get(5), p$get(6))
p$set(1, l)
},
p_comp_expression_5 =
function(doc="comp_expression : comp_expression ',' NAME NUM NUM", p) {
l <- p$get(2)
if(!is.list(l)) l <- list(l)
l[[length(l) + 1]] <- c(p$get(4), p$get(5), p$get(6))
p$set(1, l)
},
p_comp_expression_6 =
function(doc="comp_expression : comp_expression ',' NEWLINE NAME NUM NUM",
p) {
l <- p$get(2)
if(!is.list(l)) l <- list(l)
l[[length(l) + 1]] <- c(p$get(5), p$get(6), p$get(7))
p$set(1, l)
},
p_error = function(p) {
if(is.null(p)) stop("Marker file error. Syntax error at EOF")
else stop(sprintf("Marker file error. Syntax error '%s' at or near line number %s\n",
p$value, self[["linenum"]]))
}
)
)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.