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);