exportRcade(x, directory="RcadeOutput", cutoffMode="top", cutoffArg = 1000, justGeneID=FALSE, removeDuplicates="beforeCutoff")Rcade object.
character - The directory to export output to.
character - The method to cut off each list (see Details). Must be "all", "top", "B" or "FDR".
numeric - What cutoff to use (see Details).
logical - if TRUE, export only the geneID column. If FALSE, export all columns.
character - Should we remove duplicate GeneIDs and, if so, should we do this before or after applying the cutoff? Must be "beforeCutoff", "afterCutoff" or "none". (If removing duplicates then, for each list, the entry with the highest B value is retained.)
exportRcade(x, directory="RcadeOutput", cutoffMode="top", cutoff = 100, justGeneID=FALSE, removeDuplicates="beforeCutoff", ...)
| File: | ChIP: |
| DE | ChIP.csv |
| Present (needs log ratio > 0) | Ignored |
| ChIPonly.csv | Present (needs log ratio > 0) |
| Absent | DEandChIP.csv |
| Present (needs log ratio > 0) | Present |
| DownChIP.csv | Present (needs log ratio > 0) |
| Present (logFC < 0) | Down.csv |
| Ignored | Present (logFC < 0) |
| DownNoChIP.csv | Absent |
| Present (logFC < 0) | Nothing.csv |
| Absent | Absent |
| UpChIP.csv | Present (needs log ratio > 0) |
| Present (logFC > 0) | Up.csv |
| Ignored | Present (logFC > 0) |
| UpNoChIP.csv | Absent |
| Present (logFC > 0) | File: |
Each file contains genes appropriate to its hypothesis, sorted by descending B value (i.e. ranked from most interesting to least interesting). For example, if you wanted the genes that display DE (either up or down) and also have ChIP signal present, you would look at the top rows of DEandChIP.csv. For genes that have a ChIP signal but explicitly show no DE, use ChIPonly.csv.
A cutoff is applied to each list, according to the value of cutoffMode, referring to cutoffArg if necessary:
cutoffMode = "all"cutoff ignored, all results written to disk.
cutoffMode = "top"cutoffArg.
cutoffMode = "B"B > cutoffArg, where B is the log-odds.
cutoffMode = "FDR" The cutoff chosen is the one that maximizes the value of FPR + cutoffArg*FNR.
data(RcadeSTAT1)
## Not run: exportRcade(RcadeSTAT1)
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