Difference between revisions of "VennDiagram.R"
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(New page: # This illustrates a problem with missing values library(limma) p <- 100 n <- 3 x <- matrix(0, nr=p,nc=n) set.seed(1) x[,1] <- rbinom(p, 1, 1/10) x[,2] <- rbinom(p, 1, 1/10) x[,3] <- rbi...) |
(Code update) |
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| (2 intermediate revisions by the same user not shown) | |||
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| + | <pre> | ||
# This illustrates a problem with missing values | # This illustrates a problem with missing values | ||
| + | library(limma) | ||
| + | |||
| + | graphics.off() | ||
| − | |||
p <- 100 | p <- 100 | ||
n <- 3 | n <- 3 | ||
x <- matrix(0, nr=p,nc=n) | x <- matrix(0, nr=p,nc=n) | ||
| + | colnames(x) <- LETTERS[1:3] | ||
set.seed(1) | set.seed(1) | ||
| − | + | for(i in 1:n) { | |
| − | x[, | + | x[,i] <- rbinom(p, 1, 1/10) |
| − | x | + | } |
| − | x | + | |
| + | # Two copies one containing missing information | ||
| + | x.NA <- x | ||
| − | |||
vennDiagram(x) | vennDiagram(x) | ||
| + | title("Simulated venn diagram without missing values") | ||
| + | |||
| + | x[4,] | ||
| + | x.NA[4,3] <- NA | ||
| + | |||
| − | x | + | X11() |
| + | vennDiagram(x.NA) | ||
| + | title("Simulated venn diagram with missing values") | ||
| + | # Printing output from A:B intersection | ||
vennCounts(x)[7,] | vennCounts(x)[7,] | ||
| − | + | vennCounts(x.NA)[7,] | |
| + | # Note missing value in row 7 has reduced the venn diagram count | ||
| + | # This removes all information about that observation even though we know that | ||
| + | # there was valid information about A and B in row 7, so that information had | ||
| + | # to of been either a A:B interaction or an A:B:C interaction | ||
| + | </pre> | ||
Latest revision as of 21:44, 6 August 2007
# This illustrates a problem with missing values
library(limma)
graphics.off()
p <- 100
n <- 3
x <- matrix(0, nr=p,nc=n)
colnames(x) <- LETTERS[1:3]
set.seed(1)
for(i in 1:n) {
x[,i] <- rbinom(p, 1, 1/10)
}
# Two copies one containing missing information
x.NA <- x
vennDiagram(x)
title("Simulated venn diagram without missing values")
x[4,]
x.NA[4,3] <- NA
X11()
vennDiagram(x.NA)
title("Simulated venn diagram with missing values")
# Printing output from A:B intersection
vennCounts(x)[7,]
vennCounts(x.NA)[7,]
# Note missing value in row 7 has reduced the venn diagram count
# This removes all information about that observation even though we know that
# there was valid information about A and B in row 7, so that information had
# to of been either a A:B interaction or an A:B:C interaction
