Normalise test perturbation scores by permutation

normalise_by_permu(permutedScore, testScore, pAdj_method = "fdr")

Arguments

permutedScore: A list. Output of generate_permuted_scores
testScore: A matrix. Output of weight_ss_fc
pAdj_method: Method for adjusting p-values for multiple comparisons. See ?p.adjust for methods available. Default to FDR.

Value

A dataframe.

Details

Normalise the test perturbation scores generated by weight_ss_fc through the permuted perturbation scores derived from the generate_permuted_scores function. The mean absolute deviation(MAD) and median of perturbation scores for each pathway are firstly derived from the permuted perturbation scores. The test perturbation scores are then converted to robust z-scores using MADs and medians calculated.

Examples

# \donttest{
load(system.file("extdata", "gsTopology.rda", package = "sSNAPPY"))
#> Warning: cannot open compressed file '', probable reason 'No such file or directory'
#> Error in readChar(con, 5L, useBytes = TRUE): cannot open the connection
ssPertScore <- compute_perturbation_score(ls$logFC, gsTopology)
#> Error in lapply(gsTopology, rownames): object 'gsTopology' not found
permutedScore <- generate_permuted_scores(logCPM, numOfTreat = 2,
 NB = 5, gsTopology = gsTopology, weight = ls$weight)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'expreMatrix' in selecting a method for function 'generate_permuted_scores': object 'logCPM' not found
normalisedScores <- normalise_by_permu(permutedScore, ssPertScore)
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': object 'permutedScore' not found
 # }
 # Load the example output
 load(system.file("extdata", "normalisedScores.rda", package = "sSNAPPY"))
#> Warning: cannot open compressed file '', probable reason 'No such file or directory'
#> Error in readChar(con, 5L, useBytes = TRUE): cannot open the connection
 normalisedScores
#> Error in eval(expr, envir, enclos): object 'normalisedScores' not found