RN_calc_LPV | R Documentation |
This function calculates local p-values from expression data, output as -log10(p-value).
RN_calc_LPV(X, design, bind = TRUE)
X |
data.frame with expression values. It may contain additional non numeric columns (eg. a column with gene names) |
design |
The design matrix. Refer to the help for RN_calc for further info. |
bind |
See Value (Default = TRUE) |
If bind is TRUE the function returns a data.frame with the original expression values from data.frame X and attached columns with the -log10(p-values) computed for each sample, otherwise only the matrix of -log10(p-values) is returned.
Giulio Pavesi - Dep. of Biosciences, University of Milan
Federico Zambelli - Dep. of Biosciences, University of Milan
data("RN_Brain_Example_tpm", "RN_Brain_Example_design") LPV <- RN_calc_LPV(RN_Brain_Example_tpm, RN_Brain_Example_design) ## The function is currently defined as function(X, design = NULL, bind = TRUE) { if(is.null(design)) { design <- .RN_default_design(sum(sapply(X, is.numeric))) } rnums <- sapply(X, is.numeric) .RN_design_check(X, design, rnums) RL <- .RN_get_replicate_list(design) l1 <- rep("LOC_LPV", length(X[rnums])) l2 <- colnames(X[rnums]) PV <- apply(X[rnums], 1, '.RN_calc_LPV_row', RL = RL) PV <- t(PV) colnames(PV) <- paste(l1, l2, sep="_") if(bind) { return (cbind(X, PV)) } else return (PV) }
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