Commit 4e34a954 authored by Sudeep Sahadevan's avatar Sudeep Sahadevan

fixed wierd extractRegions bug with tibbles

parent 9215ce7e
......@@ -17,6 +17,7 @@ Imports:
utils
Depends:
R(>= 3.6.0),
R.utils,
DESeq2,
BiocParallel
Suggests:
......
......@@ -6,4 +6,5 @@ Changes in version 1.0.2 (2020-02-03)
+ LRT tests to results_DEWSeq function
Changes in version 1.1.4 (2020-04-07)
+ DEWSeq version bump for Bioconductor 3.11
\ No newline at end of file
+ DEWSeq version bump for Bioconductor 3.11
+ added missing dependency R.utils
......@@ -114,6 +114,10 @@ extractRegions <- function(windowRes,
',log2FoldChangeCol,': log2foldchange column.
Missing columns: ',paste(missingCols,collapse=", "),'')
}
if(is(windowRes,'data.table') ||is(windowRes,'tbl') ){
windowRes <- data.frame(windowRes)
warning('windowRes is a data.table or tibble object, converting it to data.frame')
}
windowRes <- na.omit(windowRes[,requiredCols])
sigDat <- windowRes[ windowRes[,padjCol]<=padjThresh &
windowRes[,log2FoldChangeCol]>=log2FoldChangeThresh, ]
......
......@@ -710,7 +710,6 @@ majority of the hits are coming from histone genes.
`resultWindows` contains information about the differential expression of
windows. Now we would like to combine overlapping windows to a binding region.
```{r extractRegions, eval = TRUE, results = "hide"}
resultRegions <- extractRegions(windowRes = resultWindows,
padjCol = "p_adj_IHW",
......
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