Hi All,
I have a table with six columns (in the following).
So, I want to delete SNPs that are less than number 10 in the SNP column.
What is the best idea?
Best Regard
Mostafa
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written
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mostafarafiepour
awk !
a cmdline such as below one should do the trick:
awk ' $4 >= 10' <table-file> > new_file
and if you want to (additionally) apply calculations on a certain column:
awk ' $4 >= 10' <table-file> | awk '$2=$2+2000' > new_file
Read the file, and filter out any row where SNP column is more than or equal to 10:
data <- read.table("SNP.txt", header = TRUE)
data <- data[ data$SNP >= 10, ])
To exclude 1st BP column, and to add 20KB to BP column:
data <- data[ , -3 ]
data$BP <- data$BP + 20000
many thanks for your reply,
I could do it.
Now, I have two BP columns.
First I want to delete one of them. And the second, I want to add 20,000 to each of the numbers in the first BP column.
What is the best idea?
awk again ;)
pretty nifty stuff awk
yes, now i want to add amount 20,000 to each of the numbers in the first BP column.
for example:
1+20000
20001+20000
40001+20000
.
.
.
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written
by
mostafarafiepour
You can add other operations to the cmdline I provided earlier (or do it in one go even). I'll split it up in separate operations for increased readability and understanding
awk ' $4 >= 10' <table-file> | awk '$2=$2+2000' > new_file
why fire up R while you can simply do this command line? ;-)
OK, added it (though the question on the +20K was part of this thread).
and, OK, point taken.
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You can filter out these rows :
https://stackoverflow.com/questions/7381455/filtering-a-data-frame-by-values-in-a-column