[R] filter a tab delimited text file

[Duke]

  On 9/10/10 2:49 PM, Gabor Grothendieck wrote:
> On Fri, Sep 10, 2010 at 1:24 PM, Duke<duke.lists at gmx.com>  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).
>>
> This will copy input lines matching pattern as well as the header to
> the output verbatim preserving all quotes, spacing, etc.
>
> myFilter<- function(infile, outfile, pattern = "TRUE$") {
> 	L<- readLines(infile)
> 	cat(L[1], "\n", file = outfile)
> 	L2<- grep(pattern, L[-1], value = TRUE)
> 	for(el in L2) cat(el, "\n", file = outfile, append = TRUE)
> }
>
> # e.g.
> myFilter("infile.txt", "outfile.txt")
>

I love this the best! Even it is not as simple as the bash one liner 
(system( "cat infile.txt | grep -v FALSE > outfile.txt", wait=TRUE )), 
but I am very happy to learn that R does have other similar functions as 
in bash. If there is a document or a list of all such functions, that 
would be excellent.

Thanks Gabor,

D.