subset a defined row plus the aforegoing
On Thu, Nov 1, 2012 at 10:28 AM, Hermann Norpois
<hnorpois at googlemail.com> wrote:
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?
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
Thanks Hermann
df
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:
dput (df)
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")
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