errors in if else codes in scde.failure.probability?

[ccshao]

if("conc.a2" %in% names(models)) is used twice. Something wrong here?

scde.failure.probability <- function(models, magnitudes = NULL, counts = NULL) { if(is.null(magnitudes)) { if(!is.null(counts)) { magnitudes <- scde.expression.magnitude(models, counts) } else { stop("ERROR: either magnitudes or counts should be provided") } } if(is.matrix(magnitudes)) { # a different vector for every cell if(!all(rownames(models) %in% colnames(magnitudes))) { stop("ERROR: provided magnitude data does not cover all of the cells specified in the model matrix") } if("conc.a2" %in% names(models)) { x <- t(1/(exp(t(magnitudes)_models$conc.a +t(magnitudes^2)_models$conc.a2 + models$conc.b)+1)) } else { x <- t(1/(exp(t(magnitudes)_models$conc.a + models$conc.b)+1)) } } else { # a common vector of magnitudes for all cells

same if else statment here *_

    if**("conc.a2" %in% names(models))**{
        x <- t(1/(exp((models$conc.a %_% t(magnitudes)) + (models$conc.a2 %_% t(magnitudes^2)) + models$conc.b)+1))
    } else {
        x <- t(1/(exp((models$conc.a %*% t(magnitudes)) + models$conc.b)+1))
    }
}
x[is.nan(x)] <- 0
colnames(x) <- rownames(models)
x

}

[JEFworks]

Hi Shao,

Thanks for your concern.

Depending on whether there is a separate magnitude esimate for each cell (ie. magnitudes is a matrix) or if there is a common magnitude estimate for all cells (ie. magnitudes is a vector), we perform either matrix based operations or vector based operations.

Please see the full function below. The if("conc.a2" %in% names(models)) checks are nested in the is.matrix(magnitudes) check and are needed.

scde.failure.probability <- function(models, magnitudes = NULL, counts = NULL) {
    if(is.null(magnitudes)) {
        if(!is.null(counts)) {
            magnitudes <- scde.expression.magnitude(models, counts)
        } else {
            stop("ERROR: either magnitudes or counts should be provided")
        }
    }
    if(is.matrix(magnitudes)) { # a different vector for every cell
        if(!all(rownames(models) %in% colnames(magnitudes))) { stop("ERROR: provided magnitude data does not cover all of the cells specified in the model matrix") }
        if("conc.a2" %in% names(models)) {
            x <- t(1/(exp(t(magnitudes)*models$conc.a +t(magnitudes^2)*models$conc.a2 + models$conc.b)+1))
        } else {
            x <- t(1/(exp(t(magnitudes)*models$conc.a + models$conc.b)+1))
        }
    } else { # a common vector of magnitudes for all cells
        if("conc.a2" %in% names(models)) {
            x <- t(1/(exp((models$conc.a %*% t(magnitudes)) + (models$conc.a2 %*% t(magnitudes^2)) + models$conc.b)+1))
        } else {
            x <- t(1/(exp((models$conc.a %*% t(magnitudes)) + models$conc.b)+1))
        }
    }
    x[is.nan(x)] <- 0
    colnames(x) <- rownames(models)
    x
}

Hope this addresses your question.

Best, Jean

[ccshao]

Thanks for the quick reply! It is clear.