Hi Phil,
On 9/10/10 1:45 PM, Phil Spector wrote:
Duke -
One possibility is to check the help files for the functions
involved to see if there are options to control this behaviour.
For example, the check.names= argument to read.table, or the quote=
argument to write.table. How about
Yes, I did before posting question to the list. But somehow I missed (or
misunderstood) the check.names option. As about quote=FALSE option for
write.table, it does not work as I want, since all the headers are
unquoted too.
expFC <- read.table("test.txt", header=TRUE, sep="\t", check.names=FALSE)
expFC.TRUE <- expFC[expFC[dim(expFC)[2]]=="TRUE",]
write.table(expFC.TRUE, file="test_TRUE.txt", row.names=FALSE,
sep="\t", quote=FALSE )
This works perfectly and solves the first issue. Thanks so much Phil.
D.
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Fri, 10 Sep 2010, Duke wrote:
Hi all,
I have to filter a tab-delimited text file like below:
"GeneNames" "value1" "value2" "log2(Fold_change)"
"log2(Fold_change) normalized" "Signature(abs(log2(Fold_change)
normalized) > 4)"
ENSG00000209350 4 35 -3.81131293562629
-4.14357714689656 TRUE
ENSG00000177133 142 2 5.46771720082336
5.13545298955309 FALSE
ENSG00000116285 115 1669 -4.54130810709955
-4.87357231836982 TRUE
ENSG00000009724 10 162 -4.69995182667858
-5.03221603794886 FALSE
ENSG00000162460 3 31 -4.05126372834704
-4.38352793961731 TRUE
based on the last column (TRUE), and then write to a new text file,
meaning I should get something like below:
"GeneNames" "value1" "value2" "log2(Fold_change)"
"log2(Fold_change) normalized" "Signature(abs(log2(Fold_change)
normalized) > 4)"
ENSG00000209350 4 35 -3.81131293562629
-4.14357714689656 TRUE
ENSG00000116285 115 1669 -4.54130810709955
-4.87357231836982 TRUE
ENSG00000162460 3 31 -4.05126372834704
-4.38352793961731 TRUE
I used read.table and write.table but I am still not very satisfied
with the results. Here is what I did:
expFC <- read.table( "test.txt", header=T, sep="\t" )
expFC.TRUE <- expFC[expFC[dim(expFC)[2]]=="TRUE",]
write.table (expFC.TRUE, file="test_TRUE.txt", row.names=FALSE,
sep="\t" )
Result:
"GeneNames" "value1" "value2" "log2.Fold_change."
"log2.Fold_change..normalized"
"Signature.abs.log2.Fold_change..normalized....4."
"ENSG00000209350" 4 35 -3.81131293562629
-4.14357714689656 TRUE
"ENSG00000116285" 115 1669 -4.54130810709955
-4.87357231836982 TRUE
"ENSG00000162460" 3 31 -4.05126372834704
-4.38352793961731 TRUE
As you can see, there are two points:
1. The headers were altered. All the special characters were
converted to dot (.).
2. The gene names (first column) were quoted (which were not in the
original file).
The second point is not very annoying, but the first one is. How do I
get exact the headers like the original file?
Thanks,
D.
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and provide commented, minimal, self-contained, reproducible code.
