R help - Feb 2013 - Adding complex new columns to data frame depending on existing column

Hello

I have a data frame as below
V1     V2     V3        V4         V5 V6
chr1 18884  C         CAAAA      2  0
chr1 135419 TATACA  T          2  0
chr1 332045 T       TTG      0  2
chr1 453838 T       TAC      2  0
chr1 567652 T        TG      1  0
chr1 602541 TTTA    T          2  0

on which I want to perform complex rearrangement such that:

if V3 is a string >1 (i.e line 2) then I generate 2 new columns where
first new column = V2-1 & second new column = V2+(length of string in V3)+1

therefore, for line 2 output would look like:
chr1 135419 TATACA  T   2  0 135418 135426

if length of string in V3 = 1 and V4=string of length>1 (i.e. line 1) then
first new column = V2 & second new column = V2+2

output for line 1 would be:
chr1 18884  C         CAAAA      2  0 18884  18886

I am not sure:
a) how to use R to substitute the length of the string in V3 with the
number representing this length
b) whether apply would be best to use here
Thanks

	[[alternative HTML version deleted]]

Hi,

May be this helps:
df1<-read.table(text="
V1 ? ?V2 ? ?V3 ? ? ? ?V4 ? ? ? ?V5 V6
chr1 18884 ?C ? ? ? ?CAAAA ? ? ?2 ?0
chr1 135419 TATACA ?T ? ? ? ? ?2 ?0
chr1 332045 T ? ? ?TTG ? ? ?0 ?2
chr1 453838 T ? ? ?TAC ? ? ?2 ?0
chr1 567652 T ? ? ? ?TG ? ? ?1 ?0
chr1 602541 TTTA ? ?T ? ? ? ? ?2 ?0
",header=TRUE,sep="",stringsAsFactors=FALSE)
?df1$newCol1<- ifelse(nchar(df1$V3)>1,df1$V2-1,ifelse(nchar(df1$V3)==1
& nchar(df1$V4)>1, df1$V2,NA))?
?df1$newCol2<-
ifelse(nchar(df1$V3)>1,df1$V2+nchar(df1$V3)+1,ifelse(nchar(df1$V3)==1 &
nchar(df1$V4)>1, df1$V2+2,NA))?


df1
# ? ?V1 ? ? V2 ? ? V3 ? ?V4 V5 V6 newCol1 newCol2
#1 chr1 ?18884 ? ? ?C CAAAA ?2 ?0 ? 18884 ? 18886
#2 chr1 135419 TATACA ? ? T ?2 ?0 ?135418 ?135426
#3 chr1 332045 ? ? ?T ? TTG ?0 ?2 ?332045 ?332047
#4 chr1 453838 ? ? ?T ? TAC ?2 ?0 ?453838 ?453840
#5 chr1 567652 ? ? ?T ? ?TG ?1 ?0 ?567652 ?567654
#6 chr1 602541 ? TTTA ? ? T ?2 ?0 ?602540 ?602546
A.K.
----- Original Message -----
From: Tom Oates <toates19 at gmail.com>
To: r-help at r-project.org
Cc: 
Sent: Sunday, February 3, 2013 12:20 PM
Subject: [R] Adding complex new columns to data frame depending on existing
column

Hello

I have a data frame as below
V1? ?  V2? ?  V3? ? ? ? V4? ? ? ?  V5 V6
chr1 18884? C? ? ? ?  CAAAA? ? ? 2? 0
chr1 135419 TATACA? T? ? ? ? ? 2? 0
chr1 332045 T? ? ?  TTG? ? ? 0? 2
chr1 453838 T? ? ?  TAC? ? ? 2? 0
chr1 567652 T? ? ? ? TG? ? ? 1? 0
chr1 602541 TTTA? ? T? ? ? ? ? 2? 0

on which I want to perform complex rearrangement such that:

if V3 is a string >1 (i.e line 2) then I generate 2 new columns where
first new column = V2-1 & second new column = V2+(length of string in V3)+1

therefore, for line 2 output would look like:
chr1 135419 TATACA? T?  2? 0 135418 135426

if length of string in V3 = 1 and V4=string of length>1 (i.e. line 1) then
first new column = V2 & second new column = V2+2

output for line 1 would be:
chr1 18884? C? ? ? ?  CAAAA? ? ? 2? 0 18884? 18886

I am not sure:
a) how to use R to substitute the length of the string in V3 with the
number representing this length
b) whether apply would be best to use here
Thanks

??? [[alternative HTML version deleted]]

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