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Merge pull request #50 from VEuPathDB/add-differential-expression
Add differential expression
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
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| check_comparator <- function(object) { | ||
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| variable <- object@variable | ||
| groupA <- object@groupA | ||
| groupB <- object@groupB | ||
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| errors <- character() | ||
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| # Check that the variable has a reasonable variable spec | ||
| if (is.na(variable@variableSpec@variableId)) { | ||
| msg <- "Comparator variable needs a variable id" | ||
| errors <- c(errors, msg) | ||
| } | ||
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| # Check that groups exist | ||
| if (!length(groupA) || !length(groupA)) { | ||
| msg <- "Both groupA and groupB must be defined" | ||
| errors <- c(errors, msg) | ||
| } | ||
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| if (identical(variable@dataShape@value, "CONTINUOUS")) { | ||
| ## Checks for continuous variables | ||
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| # Err if variable is continuous but either group is missing a binStart or binEnd | ||
| if (!all(unlist(lapply(groupA, function(bin) {return(!!length(bin@binStart))})))) { | ||
| msg <- "All groupA bins must have a binStart" | ||
| errors <- c(errors, msg) | ||
| } | ||
| if (!all(unlist(lapply(groupA, function(bin) {return(!!length(bin@binEnd))})))) { | ||
| msg <- "All groupA bins must have a binEnd" | ||
| errors <- c(errors, msg) | ||
| } | ||
| if (!all(unlist(lapply(groupB, function(bin) {return(!!length(bin@binStart))})))) { | ||
| msg <- "All groupB bins must have a binStart" | ||
| errors <- c(errors, msg) | ||
| } | ||
| if (!all(unlist(lapply(groupB, function(bin) {return(!!length(bin@binEnd))})))) { | ||
| msg <- "All groupB bins must have a binEnd" | ||
| errors <- c(errors, msg) | ||
| } | ||
| } else { | ||
| ## Checks for non-continuous variables | ||
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| # Ensure no values are duplicated between group A and group B | ||
| groupAValues <- getGroupLabels(object, "groupA") | ||
| groupBValues <- getGroupLabels(object, "groupB") | ||
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| if (!!length(intersect(groupAValues, groupBValues))) { | ||
| msg <- "groupA and groupB cannot share members" | ||
| errors <- c(errors, msg) | ||
| } | ||
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| } | ||
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| return(if (length(errors) == 0) TRUE else errors) | ||
| } | ||
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| #' Comparator | ||
| #' | ||
| #' A class for representing a variable that will be used to compare samples between two groups. The variable's | ||
| #' values will be used to split samples into groups. | ||
| #' | ||
| #' @slot variable A VariableMetadata | ||
| #' @slot groupA BinList | ||
| #' @slot groupB BinList | ||
| #' @name Comparator-class | ||
| #' @rdname Comparator-class | ||
| #' @include class-VariableMetadata.R | ||
| #' @export | ||
| Comparator <- setClass("Comparator", representation( | ||
| variable = 'VariableMetadata', | ||
| groupA = 'BinList', | ||
| groupB = 'BinList' | ||
| ), prototype = prototype( | ||
| variable = new("VariableMetadata"), | ||
| groupA = new("BinList"), | ||
| groupB = new("BinList") | ||
| ), validity = check_comparator) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| check_count_data_collection <- function(object) { | ||
| errors <- character() | ||
| df <- object@data | ||
| record_id_col <- object@recordIdColumn | ||
| ancestor_id_cols <- object@ancestorIdColumns | ||
| all_id_cols <- c(record_id_col, ancestor_id_cols) | ||
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| allDataColsNumeric <- all(unlist(lapply(df[, !(names(df) %in% c(record_id_col, ancestor_id_cols))], is.numeric))) | ||
| if (inherits(df, 'data.table')) allDataColsNumeric <- all(unlist(lapply(df[, !(names(df) %in% c(record_id_col, ancestor_id_cols)), with=F], is.numeric))) | ||
| if (!allDataColsNumeric) { | ||
| msg <- paste("All columns except the ID columns must be numeric.") | ||
| errors <- c(errors, msg) | ||
| } | ||
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| numeric_data <- df[, !(names(df) %in% all_id_cols)] | ||
| if (inherits(df, 'data.table')) numeric_data <- df[, !(names(df) %in% all_id_cols), with=F] | ||
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| if (!identical(numeric_data, round(numeric_data))) { | ||
| msg <- "Count data must be integer numbers." | ||
| errors <- c(errors, msg) | ||
| } | ||
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| if (any(df < 0, na.rm=TRUE)) { | ||
| msg <- paste("Count data cannot contain negative values.") | ||
| errors <- c(errors, msg) | ||
| } | ||
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| return(if (length(errors) == 0) TRUE else errors) | ||
| } | ||
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| #' Count Data | ||
| #' | ||
| #' A class for working with count data, including microbial or genetic assays. | ||
| #' | ||
| #' @slot data A data.frame of integer abundance counts with genes (species, etc.) as columns and samples as rows | ||
| #' @slot sampleMetadata A data.frame of metadata about the samples with samples as rows and metadata variables as columns | ||
| #' @slot recordIdColumn The name of the column containing IDs for the samples. All other columns will be treated as abundance values. | ||
| #' @slot ancestorIdColumns A character vector of column names representing parent entities of the recordIdColumn. | ||
| #' @slot imputeZero A logical indicating whether NA/ null values should be replaced with zeros. | ||
| #' @name CountDataCollection-class | ||
| #' @rdname CountDataCollection-class | ||
| #' @include class-CollectionWithMetadata.R | ||
| #' @export | ||
| CountDataCollection <- setClass("CountDataCollection", contains = "CollectionWithMetadata", validity = check_count_data_collection) |
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