Entering edit mode
3.9 years ago
prithvi.mastermind
▴
50
I'm using pamr function for training my model and thereby predicting on my test data. I have written the code but I'm not sure if my code is correct or not? Please give valuable feedback.
library(pamr)
data1 <- read.table("DISCOVERY_INPUT.txt",sep="\t")
vecto <- scan("DISC_LABELS.txt", character(), quote = "")
mydata <- list(x=data1,y=vecto)
mytrain <- pamr.train(mydata)
mycv <- pamr.cv(mytrain,mydata)
pamr.plotcv(mycv)
####Testing with my trained model object on test data##
newx1 <- as.matrix(read.table("CELL_LINE_INPUT.txt",sep="\t"))
prediction_result <- pamr.predict(mytrain, newx1, threshold = 1.5)
View(prediction_result)
Input Data:
DISC_LABELS (Here 1,2,3 represents cluster class in which our samples are present)
2 1 1 2 1 3 1 1 3 1 1 2 2 1 3 1 2 1 1 3
DISCOVERY_INPUT
0.226914999 0.17475025 0.223162558 0.268781674 0.276437497 0.157510059 0.202060238 0.168054062 0.223642002 0.144085457 0.155465769 0.131518003 0.188500606 0.275243912 0.178517605 0.164768752 0.169705693 0.114435576 0.13449927 0.143942181
CELL_LINE_INPUT (My test data/cell line data)
0.275104129 0.296965021 0.311240317 0.291522787 0.477223901 0.38288832 0.257801771 0.569291942 0.280361337 0.477443593 0.356490082 0.664772161 0.46293188 0.334071418 0.32811604 0.384570387 0.332922032 0.283945342 0.29626007 0.347386226 0.31456261 0.289693393 0.278474175 0.322551733 0.309029375 0.38502583 0.451128247 0.293995882 0.350323047 0.322005762 0.356336858 0.431325481 0.338219893 0.460566981 0.314755048 0.268779623 0.300202576 0.399101138 0.368131084 0.403293509 0.445137823 0.292816452 0.357048084 0.243247269 0.360730309 0.361357446 0.519835095 0.280882086 0.282587769 0.378009164 0.31190293
