thanks Richie. It woks perfectly.
----- Original Message ----
From: "[EMAIL PROTECTED]" <[EMAIL PROTECTED]>
To: joseph <[EMAIL PROTECTED]>
Cc: r-help@r-project.org; [EMAIL PROTECTED]
Sent: Wednesday, February 6, 2008 2:22:16 AM
Subject: Re: [R] inserting text lines in a dat frame
>
I
am
trying
to
prepare
a
bed
file
to
load
as
accustom
track
on
the
>
UCSC
genome
browser.
>
I
have
a
data
frame
that
looks
like
the
one
below.
>
>
x
>
V1
V2
V3
>
1
chr1
11255
55
>
2
chr1
11320
29
>
3
chr1
11400
45
>
4
chr2
21680
35
>
5
chr2
21750
84
>
6
chr2
21820
29
>
7
chr2
31890
46
>
8
chr3
32100
29
>
9
chr3
52380
29
>
10
chr3
66450
46
>
I
would
like
to
insert
the
following
4
lines
at
the
beginning:
>
browser
position
chr1:1-10000
>
browser
hide
all
>
track
type=wiggle_0
name=sample
description=chr1_sample
visibility=full
>
variableStep
chrom=chr1
span=1
>
and
then
insert
2
lines
before
each
chromosome:
>
track
type=wiggle_0
name=sample
description=chr2_sample
visibility=full
>
vriableStep
chrom=chr2
span=1
>
The
final
result
should
be
tab
delimited
file
that
looks
like
this:
>
browser
position
chr1:1-10000
>
browser
hide
all
>
track
type=wiggle_0
name=sample
description=chr1_sample
visibility=full
>
variableStep
chrom=chr1
span=1
>
chr1
11255
55
>
chr1
11320
29
>
chr1
11400
45
>
track
type=wiggle_0
name=sample
description=chr2_sample
visibility=full
>
variableStep
chrom=chr2
span=1
>
chr2
21680
35
>
chr2
21750
84
>
chr2
21820
29
>
track
type=wiggle_0
name=sample
description=chr3_sample
visibility=full
>
variableStep
chrom=chr3
span=1
>
chr3
32100
29
>
chr3
32170
45
>
chr3
32240
45
#First
write
your
preamble
text
to
a
file
preamble
<-
c("browser
position
chr1:1-10000",
"browser
hide
all",
"track
type=wiggle_0
name=sample
description=chr1_sample
visibility=full",
"variableStep
chrom=chr1
span=1")
write(preamble,
"myfile.txt")
#Now
split
your
data
frame
up
by
the
values
in
V1
x
<-
data.frame(V1=rep(c("chr1",
"chr2",
"chr3"),times=c(3,4,3)),
V2=c(11255,11320,11400,21680,21750,21820,21890,32100,52380,66450),V3=c(55,29,45,35,84,29,46,29,29,46))
spx
<-
split(x,
x$V1)
#Create
lines
of
text
to
go
before
each
piece
of
data
frame
lV1
<-
levels(x$V1)
maintext
<-
paste("track
type=wiggle_0
name=sample
description=",
lV1,
"_sample
visibility=full\nvariableStep
chrom=",
lV1,
"
span=1",
sep="")
#Use
a
loop
to
write
the
pieces
to
the
file
for(i
in
1:
nlevels(x$V1))
{
write(maintext[i],
"myfile.txt",
append=TRUE)
write.table(spx[[i]],
"myfile.txt",
append=TRUE,
sep="\t",
quote=FALSE,
col.names=FALSE,
row.names=FALSE)
}
Regards,
Richie.
Mathematical
Sciences
Unit
HSL
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