MIGSAres-common {MIGSA} | R Documentation |
Several R base overwritten functions to manipulate a MIGSAres object as a data.frame way. NOTE: When subsetting a MIGSAres object, if it does not have the id, GS_Name and (at least) one experiment columns, then it wont be a MIGSAres object, i.e., migsaRes[,c("id","igsaInput1")] is no longer a MIGSAres object.
## S4 method for signature 'MIGSAres' dim(x) ## S4 method for signature 'MIGSAres' x$name ## S4 method for signature 'MIGSAres' colnames(x) ## S4 method for signature 'MIGSAres' head(x, n = 6L) ## S4 method for signature 'MIGSAres' tail(x, n = 6L) ## S4 method for signature 'MIGSAres,ANY,ANY,ANY' x[i, j, drop = FALSE] ## S4 method for signature 'MIGSAres' show(object) ## S4 method for signature 'MIGSAres' as.data.frame(x) ## S4 method for signature 'MIGSAres,MIGSAres' merge(x, y)
x |
MIGSAres object. |
name |
as used in |
n |
as used in |
i |
as used in |
j |
as used in |
drop |
as used in |
object |
MIGSAres object. |
y |
MIGSAres object. |
Desired object.
data(migsaRes) ## As we ran MIGSA for two experiments and 200 gene sets, it must have 200 ## rows, and five columns (id, Name, GS_Name, and the experiments names). dim(migsaRes) ## migsaRes shown as data.frame has these column names: id, Name, GS_Name, ## and the experiments names. As we ran two experiments, names igsaInput1 ## and igsaInput2, we can use $ in these ways: head(migsaRes$id) table(migsaRes$Name) table(migsaRes$GS_Name) head(migsaRes$igsaInput1) head(migsaRes$igsaInput2) colnames(migsaRes) head(migsaRes) ## Or see the first 10 head(migsaRes, n = 10) tail(migsaRes) ## Or see the last 10 tail(migsaRes, n = 10) ## migsaRes shown as data.frame has these column names: id, Name, GS_Name, ## and the experiments names. As we ran two experiments, names igsaInput1 ## and igsaInput2, we can use [ in these ways: ## Lets get the first 5 rows and 4 columns (the result is a MIGSAres object). migsaRes[1:5, 1:4] class(migsaRes[1:5, 1:4]) ## Lets get the experiments results. Note that this is not any more a ## MIGSAres object. migsaRes[, c("igsaInput1", "igsaInput2")] class(migsaRes[, c("igsaInput1", "igsaInput2")]) migsaRes migsaResDFrame <- as.data.frame(migsaRes) head(migsaResDFrame) migsaRes1 <- migsaRes[, 1:4] migsaRes2 <- migsaRes[, c(1:3, 5)] migsaResMerged <- merge(migsaRes1, migsaRes2)