R/correctness.R

In TRONCO: TRONCO, an R package for TRanslational ONCOlogy

#### TRONCO: a tool for TRanslational ONCOlogy
####
#### Copyright (c) 2015-2017, Marco Antoniotti, Giulio Caravagna, Luca De Sano,
#### Alex Graudenzi, Giancarlo Mauri, Bud Mishra and Daniele Ramazzotti.
####
#### All rights reserved. This program and the accompanying materials
#### are made available under the terms of the GNU GPL v3.0
#### which accompanies this distribution.


#' Check if 'x' is compliant with TRONCO's input: that is if it has dataframes 
#' x$genotypes, x$annotations, x$types and x$stage (optional)
#' @title is.compliant
#' 
#' @examples
#' data(test_dataset)
#' is.compliant(test_dataset)
#' 
#' @param x A TRONCO compliant dataset.
#' @param err.fun string which identifies the function which called is.compliant
#' @param stage boolean flag to check x$stage datagframe
#' @return on error stops the computation
#' @export is.compliant
#' @importFrom utils head
#' 
is.compliant <- function(x,
                         err.fun = '[ERR]',
                         stage = !(all(is.null(x$stages)) || all(is.na(x$stages)))) {
    ## Check if x is defined.
    
    if (is.null(x) || all(is.na(x)))
        stop(paste(err.fun, ': input \'x\' is null.'))

    ## Check then if x is a list.
    
    if (!is.list(x))
        stop(paste(err.fun, ': input \'x\' is not a list.'))

    ## Check then if x has required fields.
    
    if (is.null(x$genotypes) || any(is.na(x$genotypes)))
        stop(paste(err.fun, ': input \'x\' has no genotypes field.'))   
    else if (!is.matrix(x$genotypes) && !is.data.frame(x$genotypes))
        stop(paste(err.fun, ': attribute genotypes in  \'x\' is not a matrix.'))
        
    colnames(x$annotations) = c('type', 'event')
    colnames(x$types) = c('color')
    
    ## Check if annotations table is well-formed
    
    if (is.null(x$annotations) || any(is.na(x$annotations)))
        stop(paste(err.fun, ': input \'x\' has no annotations field.'))
    else if (!is.matrix(x$annotations) && !is.data.frame(x$annotations))
        stop(paste(err.fun, ': attribute annotations in  \'x\' is not a matrix.'))
    if (!is.character(x$annotations)) {
        stop(paste(err.fun, ': attribute annotations in \'x\' is not a matrix of character.'))
    }

    ## Check if annotations table is well-formed

    if (is.null(x$types) || any(is.na(x$types)))
        stop(paste(err.fun, ': input \'x\' has no types field.'))
    else if (!is.matrix(x$types) && !is.data.frame(x$types))
        stop(paste(err.fun, ': attribute types in  \'x\' is not a matrix.'))
        
    if (stage == TRUE && (is.null(x$stages) || all(is.na(x$stages))))
        stop(paste(err.fun, ': input \'x\' has no stage field.'))
    else if (stage == TRUE && !is.matrix(x$stages) && !is.data.frame(x$stages))
        stop(paste(err.fun, ': attribute stage in  \'x\' is not a matrix.'))    

    ## Annotations sould be present for all genotypes columns.
    
    if (nrow(x$annotations) != ncol(x$genotypes) ) 
        stop(paste(err.fun, ': input \'x\' has less annotations than expected.'))           
    if (!all(colnames(x$genotypes) == rownames(x$annotations))) 
        stop(paste(err.fun, ': input \'x\' has inconsistent annotations.'))         

    ## Types should be defined for every annotation.
    
    if (nrow(x$types) != length(unique(x$annotations[,1]))) {
        message('[ERROR] rownames(x$types):',
                paste(rownames(x$types), collapse = ', ', sep = ''))
        message('[ERROR] Annotated event types:',
                paste(unique(x$annotations[,1]), collapse = ', ', sep = ''))
        
        stop(paste(err.fun, ': input \'x\' has less types than expected.'))         
    }
    
    if (!all(unique(x$annotations[,'type']) %in% rownames(x$types))) {
        stop(paste(err.fun,
                   ': input \'x\' has inconsistent types (', 
                   paste(unique(x$annotations[,'type']), collapse = ','),
                   ' vs ',
                   paste(rownames(x$types), collapse=','),
                   ').', 
                   sep = ''))               
    }

    ## Stage should be defined for every samples.
    
    if (stage == TRUE && nrow(x$stages) != nrow(x$genotypes)) 
        stop(paste(err.fun, ': input \'x\' has less stages than expected.'))            
    if (stage == TRUE && !all(rownames(x$stages) == rownames(x$genotypes))) 
        stop(paste(err.fun, ': input \'x\' has inconsistent stages.'))          
    
    if (stage == TRUE)  colnames(x$stages) = c('stage')
    
    dup = duplicated(x$annotations)
    if (any(dup)) {
        cat("Duplicated events in \'x\': \n")
        print(head(x$annotations[dup, ]))
        stop('Duplicated events.')
    }
}

# Check if x is a valid TRONCO model
# @title is.model
# @param x A TRONCO compliant dataset.
#
is.model <- function(x) {
    if (!'model' %in% names(x))
        stop('Input object is not a TRONCO model.')
}

# Check if y is a valid event list for x
# @title is.events.list
# @param x A TRONCO compliant dataset.
# @param y A TRONCO event list
#
is.events.list <- function(x, y) {
    if (!is.matrix(y))
        stop('Events should be given as matrix - see "as.events".')
    
    if (ncol(y) != 2 || !all(c('type', 'event') %in% colnames(y)))
        stop('Events are missing column "type" (type of event) or "event" (gene symbol) - see "as.events".')
    
    if (!all(rownames(y) %in% colnames(x$genotypes))) 
        stop('Events rownames are not valid keys for genotypes - see "as.events".')
}


#### end of file -- correctness.R