[R] R-code help for filtering with for loop

[ONKELINX, Thierry]

Dear John,

It looks like you are stuck in both the second and the third circle of
the R inferno (http://www.burns-stat.com/pages/Tutor/R_inferno.pdf)

You problem is easy to vectorise.

#could the number of columns >= 64 in each row
NumCols <- rowSums(datax >= 64)
#select rows with at least one column >= 64
datax[NumCols >= 1, ]

HTH,

Thierry


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium 
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be 
www.inbo.be 

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens John Antonydas Gaspar
Verzonden: maandag 2 maart 2009 11:31
Aan: r-help at r-project.org
Onderwerp: [R] R-code help for filtering with for loop

Dear Sir / Madam,

I am new for R coding. Kindly help me out in sorting out the following
problem.

There are 50 rows with six coloumns(you could see in the attached .txt
file). I
wish to go for filtering this 50 rows for any one of the six coloumns
satisfying the value >= 64.

I need to have a final table with rows having >= 64 value in any one of
the six
coloumns and the rest could be <=64. For this purpose I use the
following R
code;
---------------
datax<-read.table("filter_test.txt",row.names=1,sep="\t",header=TRUE,dec
=
".",as.is =TRUE,na.strings = "NA", colClasses = NA,check.names =
FALSE,strip.white = FALSE, blank.lines.skip = TRUE,
allowEscapes = FALSE, flush = FALSE,encoding = "unknown")


filter<-datax[,1:6]

filtered<-vector()

for(i in 1:(dim(filter)[1]))
{
for(j in 1:(dim(filter)[2]))
{
x=(filter[i,j])>=64
filtered[i]<-x
}
}

# summing the result of the above
sum(filtered)


which(filtered)
z<-which(filtered)
filereddata<-filter[z,]


write.table(filtereddata,file ="filterdgenes.txt",quote = TRUE, sep =
"\t ",
            dec = ".",row.names=T,col.names = NA, qmethod = c (escape",
"double"))

---------------------------


There is something is missing in my coding therefore the filteration is
done
according to the value of the last column that is the sixth coloumn
value not
takiing into consideration the rest of the coloumns.

For example with the table in .txt file I have attached, the first
coloumn has
29 rows having values >= 64 but the last coloumn has only 25 rows.

The filtered list should have around 29 rows but only 25 since the
coding has
considered only the last coloumn.  How to sort out this problem. Kindly
help me
out.

Thanking in advance,
With Regards,

antony


-- 
Thony
University of Cologne
50931 Cologne/Germany

Tel:  004922125918042
Handy:   004917683142627





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