Commit 69b7b59e authored by Hugo  VARET's avatar Hugo VARET

report

parent 4f9cc5fb
......@@ -284,8 +284,8 @@ Parameter values used for this analysis are:
- Conditions: `r Conditions`
- Method: `r method`
- Normalisation: `r ifelse(is.null(spikes), normalisation, "Spike-in")`
- Spikes: `r ifelse(is.null(spikes), "NULL", spikes)`
- batch: `r batch`
- Spikes: `r if (is.null(spikes)) "NULL" else spikes`
- batch: `r if (is.null(batch)) "NULL" else batch`
- alpha: `r alpha`
- pAdjustMethod: `r pAdjustMethod`
......
file <- "K4Me3_MOUSE_CuU_Peak.mtx"
Conditions <- c("C","C","U","U")
method <- "DESeq2" # Limma or DESeq2
method <- "Limma" # Limma or DESeq2
normalisation <- "scale" # "scale"
spikes <- c(0.8, 1.2, 1.1, 0.8)
spikes <- NULL # c(0.8, 1.2, 1.1, 0.8)
pAdjustMethod <- "BH"
alpha <- 0.05
batch <- c("R1","R2","R1","R2") # NULL
batch <- NULL # c("R1","R2","R1","R2")
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