Description Usage Arguments Value Author(s) Examples
FastCoxlasso help do a plot-based penalized Cox regression model via lasso algrithm.
1 2 3 4 5 6 7 8 9 10 11 | FastCoxlasso(
expr.matrix,
design,
select,
event.status=c("TTR.status","DFS.status","OS.status")[2],
event.time=c("TTR.time","DFS.time","OS.time")[2],
event.lower =c(89,89,89),
lambda.n = 3,ln.lambda = 0,label=F,
digits = 5,
names = "love"
)
|
expr.matrix |
expression matrix |
design |
design object |
select |
selected markers or genes |
event.status |
colnames of event status |
event.time |
colnames of event time |
event.lower |
the lower limit of event time |
lambda.n |
the counts of genes with parameters you want |
ln.lambda |
ln(lambda) |
label |
whether to show the genes label on the plot.Default is F |
digits |
the digits of model coefficient |
names |
part of saved files name |
a list containing gene-based survival data and model data
Weibin Huang<654751191@qq.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | ## This is a simulative process and NOT RUN
expr.matrix = train.fpkm
design = design.train
select = rocgenes
event.status="DFS.status"
event.time="DFS.time"
event.lower = 89
label = T
label=TRUE
digits = 5
names = "love"
CO1 <- FastCoxlasso(expr.matrix,
design,
select,
event.status,
event.time,
event.lower,
lambda.n = 5,
ln.lambda= -3.55,
label,digits,names)
View(CO1$DFS$modeldata)
## Common Use
FC1 <- FastCoxlasso(expr.matrix = train.fpkm,
design= design.train,
select = rocgenes,
event.status="DFS.status",
event.time="DFS.time",
event.lower= 89,
lambda.n = 5,
ln.lambda= -3.55,
names = "train")
|
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