Execute SAMSeq gene Expression analysis to count data

Execute SAMSeq gene Expression analysis to count data

Usage

runSamSeq(
  countMatrix,
  designExperiment,
  respType = "Two class unpaired",
  numberPermutations = 100
)

Arguments

countMatrix

either a matrix of raw (read) counts.

designExperiment

replicate and treatment by samples

respType

Problem type: "Quantitative" for a continuous parameter; "Two class unpaired" for two classes with unpaired observations; "Survival" for censored survival outcome; "Multiclass": more than 2 groups; "Two class paired" for two classes with paired observations.

numberPermutations

Number of permutations used to estimate false discovery rates

Value

SAMSeq report in data Frame

Examples

data(gse95077)
treats = c("BM", "JJ")
toolResult <- NULL
toolResult$samseq <- runSamSeq(countMatrix = gse95077,
                               designExperiment = rep(treats, each = 3))
#> Estimating sequencing depths...
#> Resampling to get new data matrices...
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#> Number of thresholds chosen (all possible thresholds) = 7
#> Getting all the cutoffs for the thresholds...
#> Getting number of false positives in the permutation...