I have a file in which the second column contains values of interest. I'm attempting to loop through a set of numbers (n) and get it to count the number of times a value within the range n-5:n+5 occurs in that column using R. I then wish to output that to a .csv (but haven't written that into the code so far).
I've been using:
library(expss)
SNP_file <- read.csv("testdata.csv", header = FALSE, sep = "\t")
for (n in 31130:31150) {
SNP_Number <- 0
SNP_Number <- count_if(n-5:n+5, SNP_file$V2)
df <- data.frame(column1 = c(n), column2 = c(SNP_Number))
print(df)
}
In testdata.csv there are values of 31140 and 31141 in the second column.
This returns an output like:
column1 column2
1 31130 1
column1 column2
1 31131 1
column1 column2
1 31132 1
column1 column2
1 31133 1
column1 column2
1 31134 1
column1 column2
1 31135 1
column1 column2
1 31136 1
column1 column2
1 31137 1
column1 column2
1 31138 1
column1 column2
1 31139 1
column1 column2
1 31140 2
column1 column2
1 31141 3
column1 column2
1 31142 3
column1 column2
1 31143 3
column1 column2
1 31144 3
column1 column2
1 31145 3
column1 column2
1 31146 3
column1 column2
1 31147 3
column1 column2
1 31148 3
column1 column2
1 31149 3
column1 column2
1 31150 3
But this starts out by erroneously recording an initial value of 1 where should be a value of 0, which just increases each time n goes more than another value in testdata.csv, and does not drop back to 0 once n has no values within the range n-5:n+5.
So it should look like:
column1 column2
1 31130 0
column1 column2
1 31131 0
column1 column2
1 31132 0
column1 column2
1 31133 0
column1 column2
1 31134 0
column1 column2
1 31135 1
column1 column2
1 31136 2
column1 column2
1 31137 2
column1 column2
1 31138 2
column1 column2
1 31139 2
column1 column2
1 31140 2
column1 column2
1 31141 2
column1 column2
1 31142 2
column1 column2
1 31143 2
column1 column2
1 31144 2
column1 column2
1 31145 2
column1 column2
1 31146 1
column1 column2
1 31147 0
column1 column2
1 31148 0
column1 column2
1 31149 0
column1 column2
1 31150 0
What am I doing wrong here?
Try this:
vec <- c(22761L, 31140L, 31141L, 36701L, 44108L, 46917L, 51958L, 53661L, 119844L, 119845L, 184836L, 195026L, 249733L, 251024L, 271357L, 287257L, 360638L, 382559L, 384590L, 399027L)
sapply(31130:31150, function(z) sum( (z-5) <= vec & vec <= (z+5) ))
# [1] 0 0 0 0 0 1 2 2 2 2 2 2 2 2 2 2 1 0 0 0 0