| ... | ... |
@@ -53,6 +53,12 @@ MRcoefs<-function(obj,by=2,coef=NULL,number=10,taxa=obj@taxa, |
| 53 | 53 |
uniqueNames=FALSE,adjustMethod="fdr",alpha=0.1, |
| 54 | 54 |
group=0,eff=0,numberEff=FALSE,counts=0,file=NULL){
|
| 55 | 55 |
|
| 56 |
+ if (adjustMethod == "ihw-ubiquity" || adjustMethod == "ihw-abundance") {
|
|
| 57 |
+ if (!require(IHW)) {
|
|
| 58 |
+ stop("Adjustment using IHW for adjustment requires the 'IHW' package. Please install.")
|
|
| 59 |
+ } |
|
| 60 |
+ } |
|
| 61 |
+ |
|
| 56 | 62 |
if(length(grep("fitFeatureModel",obj@call))){
|
| 57 | 63 |
groups = factor(obj@design[,by]) |
| 58 | 64 |
by = "logFC"; coef = 1:2; |
