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subset a defined row plus the aforegoing

4 messages · Hermann Norpois, Peter Langfelder, arun

Peter Langfelder
# 
On Thu, Nov 1, 2012 at 10:28 AM, Hermann Norpois
<hnorpois at googlemail.com> wrote:
With enough money and manpower, everything is possible.

This one is possible even without a whole lot of manpower or money :)
First, get rid of all rows that are neither expression not DNase since
you don't seem to want those:

df1 = df[ df$type %in% c("Expresssion", "DNase HS"), ];

#Then select all Expression rows and the immediately preceding DNase HS rows:

keep.expr = df1$type=="Expresssion";
n = nrow(df1)
keep.DNase = c(df1$type[-1]=="Expresssion" & df1$type[-n]=="DNase HS", FALSE)

# This is the result you want
result = df1[keep.expr | keep.DNase, ];

# Applied to your example:
   start.ens fc.trans        type end.ens peak end.grcm38 dpeak
1    9191942   0.9379 Expresssion      NA   NA         NA    NA
2    9191942   0.9741 Expresssion      NA   NA         NA    NA
3    9191942   0.9748 Expresssion      NA   NA         NA    NA
7   11113787       NA    DNase HS      NA   NA   11114262   279
8   11114744   0.9803 Expresssion      NA   NA         NA    NA
9   11114744   0.9904 Expresssion      NA   NA         NA    NA
12  11461513       NA    DNase HS      NA   NA   11462571   508
13  11462408   1.0129 Expresssion      NA   NA         NA    NA
14  11462408   1.0074 Expresssion      NA   NA         NA    NA
15  11489266   1.0019 Expresssion      NA   NA         NA    NA


I have to say though, the programming would be easier if you didn't
spell expression with a triple s :)

HTH,

Peter
arun
# 
Hello,

A bit confusing:
" I would like to extract
all rows (so called* defined row*s) with type==Expression - subset (df,
type==Expression) - and the aforegoing type==DNase HS (which is not
necessarly row n-1 - assumung that the defined row is n"


In the dataset, there is "Expresssion" for column "type". If you want to subset all the rows having "Expresssion" or "DNaseHS"

res<- subset(df,type=="Expresssion"|type=="DNase HS")
head(res)
#? start.ens fc.trans??????? type end.ens peak end.grcm38 dpeak
#1?? 9191942?? 0.9379 Expresssion????? NA?? NA???????? NA??? NA
#2?? 9191942?? 0.9741 Expresssion????? NA?? NA???????? NA??? NA
#3?? 9191942?? 0.9748 Expresssion????? NA?? NA???????? NA??? NA
#4?? 9195570?????? NA??? DNase HS????? NA?? NA??? 9195792?? 109
#5?? 9579854?????? NA??? DNase HS????? NA?? NA??? 9580110?? 131
#7? 11113787?????? NA??? DNase HS????? NA?? NA?? 11114262?? 279


If you don't want those rows:
subset(df,type!="Expresssion"&type!="DNase HS")
#? start.ens fc.trans type? end.ens peak end.grcm38 dpeak
#6? 11088023?????? NA p300 11088523??? 7???????? NA??? NA
A.K.




----- Original Message -----
From: Hermann Norpois <hnorpois at googlemail.com>
To: r-help at r-project.org
Cc: 
Sent: Thursday, November 1, 2012 1:28 PM
Subject: [R] subset a defined row plus the aforegoing

Hello,

my data is sorted by start.ens (see below). And now I would like to extract
all rows (so called* defined row*s) with type==Expression - subset (df,
type==Expression) - and the aforegoing type==DNase HS (which is not
necessarly row n-1 - assumung that the defined row is n). I dont know how
to add this to my subset command.

Is that possible?
Thanks Hermann
?  start.ens fc.trans? ? ? ? type? end.ens peak end.grcm38 dpeak
1? ? 9191942?  0.9379 Expresssion? ? ?  NA?  NA? ? ? ?  NA? ? NA
2? ? 9191942?  0.9741 Expresssion? ? ?  NA?  NA? ? ? ?  NA? ? NA
3? ? 9191942?  0.9748 Expresssion? ? ?  NA?  NA? ? ? ?  NA? ? NA
4? ? 9195570? ? ?  NA? ? DNase HS? ? ?  NA?  NA? ? 9195792?  109
5? ? 9579854? ? ?  NA? ? DNase HS? ? ?  NA?  NA? ? 9580110?  131
6?  11088023? ? ?  NA? ? ? ? p300 11088523? ? 7? ? ? ?  NA? ? NA
7?  11113787? ? ?  NA? ? DNase HS? ? ?  NA?  NA?  11114262?  279
8?  11114744?  0.9803 Expresssion? ? ?  NA?  NA? ? ? ?  NA? ? NA
9?  11114744?  0.9904 Expresssion? ? ?  NA?  NA? ? ? ?  NA? ? NA
10? 11114850? ? ?  NA? ? DNase HS? ? ?  NA?  NA?  11115400?  210
11? 11455056? ? ?  NA? ? DNase HS? ? ?  NA?  NA?  11455381?  175
12? 11461513? ? ?  NA? ? DNase HS? ? ?  NA?  NA?  11462571?  508
13? 11462408?  1.0129 Expresssion? ? ?  NA?  NA? ? ? ?  NA? ? NA
14? 11462408?  1.0074 Expresssion? ? ?  NA?  NA? ? ? ?  NA? ? NA
15? 11489266?  1.0019 Expresssion? ? ?  NA?  NA? ? ? ?  NA? ? NA

My (test)data:
structure(list(start.ens = c(9191942L, 9191942L, 9191942L, 9195570L,
9579854L, 11088023L, 11113787L, 11114744L, 11114744L, 11114850L,
11455056L, 11461513L, 11462408L, 11462408L, 11489266L), fc.trans =
c(0.9379,
0.9741, 0.9748, NA, NA, NA, NA, 0.9803, 0.9904, NA, NA, NA, 1.0129,
1.0074, 1.0019), type = structure(c(2L, 2L, 2L, 1L, 1L, 3L, 1L,
2L, 2L, 1L, 1L, 1L, 2L, 2L, 2L), .Label = c("DNase HS", "Expresssion",
"p300"), class = "factor"), end.ens = c(NA, NA, NA, NA, NA, 11088523L,
NA, NA, NA, NA, NA, NA, NA, NA, NA), peak = c(NA, NA, NA, NA,
NA, 7L, NA, NA, NA, NA, NA, NA, NA, NA, NA), end.grcm38 = c(NA,
NA, NA, 9195792L, 9580110L, NA, 11114262L, NA, NA, 11115400L,
11455381L, 11462571L, NA, NA, NA), dpeak = c(NA, NA, NA, 109L,
131L, NA, 279L, NA, NA, 210L, 175L, 508L, NA, NA, NA)), .Names =
c("start.ens",
"fc.trans", "type", "end.ens", "peak", "end.grcm38", "dpeak"), row.names =
c(NA,
-15L), class = "data.frame")

??? [[alternative HTML version deleted]]

______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
arun
# 
HI,
May be this also helps:res<- subset(df,type=="Expresssion"|type=="DNase HS")
res$indx<-c(0,cumsum(abs(diff(as.integer(res$type=="Expresssion")))))
res1<-with(res,aggregate(dpeak,by=list(indx=indx),tail,1,type=="DNase HS"))
res1<-res1[!is.na(res1[,2]),]
res2<-res[res$type=="Expresssion"|res[,7]%in%res1[,2],-8]
?res2
#?? start.ens fc.trans??????? type end.ens peak end.grcm38 dpeak
#1??? 9191942?? 0.9379 Expresssion????? NA?? NA???????? NA??? NA
#2??? 9191942?? 0.9741 Expresssion????? NA?? NA???????? NA??? NA
#3??? 9191942?? 0.9748 Expresssion????? NA?? NA???????? NA??? NA
#7?? 11113787?????? NA??? DNase HS????? NA?? NA?? 11114262?? 279
#8?? 11114744?? 0.9803 Expresssion????? NA?? NA???????? NA??? NA
#9?? 11114744?? 0.9904 Expresssion????? NA?? NA???????? NA??? NA
#12? 11461513?????? NA??? DNase HS????? NA?? NA?? 11462571?? 508
#13? 11462408?? 1.0129 Expresssion????? NA?? NA???????? NA??? NA
#14? 11462408?? 1.0074 Expresssion????? NA?? NA???????? NA??? NA
#15? 11489266?? 1.0019 Expresssion????? NA?? NA???????? NA??? NA
A.K.



----- Original Message -----
From: Peter Langfelder <peter.langfelder at gmail.com>
To: Hermann Norpois <hnorpois at googlemail.com>
Cc: r-help at r-project.org
Sent: Thursday, November 1, 2012 1:48 PM
Subject: Re: [R] subset a defined row plus the aforegoing

On Thu, Nov 1, 2012 at 10:28 AM, Hermann Norpois
<hnorpois at googlemail.com> wrote:
With enough money and manpower, everything is possible.

This one is possible even without a whole lot of manpower or money :)
First, get rid of all rows that are neither expression not DNase since
you don't seem to want those:

df1 = df[ df$type %in% c("Expresssion", "DNase HS"), ];

#Then select all Expression rows and the immediately preceding DNase HS rows:

keep.expr = df1$type=="Expresssion";
n = nrow(df1)
keep.DNase = c(df1$type[-1]=="Expresssion" & df1$type[-n]=="DNase HS", FALSE)

# This is the result you want
result = df1[keep.expr | keep.DNase, ];

# Applied to your example:
?  start.ens fc.trans? ? ? ? type end.ens peak end.grcm38 dpeak
1? ? 9191942?  0.9379 Expresssion? ? ? NA?  NA? ? ? ?  NA? ? NA
2? ? 9191942?  0.9741 Expresssion? ? ? NA?  NA? ? ? ?  NA? ? NA
3? ? 9191942?  0.9748 Expresssion? ? ? NA?  NA? ? ? ?  NA? ? NA
7?  11113787? ? ?  NA? ? DNase HS? ? ? NA?  NA?  11114262?  279
8?  11114744?  0.9803 Expresssion? ? ? NA?  NA? ? ? ?  NA? ? NA
9?  11114744?  0.9904 Expresssion? ? ? NA?  NA? ? ? ?  NA? ? NA
12? 11461513? ? ?  NA? ? DNase HS? ? ? NA?  NA?  11462571?  508
13? 11462408?  1.0129 Expresssion? ? ? NA?  NA? ? ? ?  NA? ? NA
14? 11462408?  1.0074 Expresssion? ? ? NA?  NA? ? ? ?  NA? ? NA
15? 11489266?  1.0019 Expresssion? ? ? NA?  NA? ? ? ?  NA? ? NA


I have to say though, the programming would be easier if you didn't
spell expression with a triple s :)

HTH,

Peter
______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.