Dear All
I now realized that it is not simple to deal with realworld problems!
This what I tried without any success:
a <- seq(1, nvar, by = 2)
b <- seq(2, nvar, by = 2)
#df2 <- transform(df2, ima1p1 = df2$x1[df2$Parent1], # Parent 1's
allele 1
#ima2p1 = df2$x2[df2$Parent1], # Parent 1's allele 2
#ima1p2 = df2$x1[df, # Parent 2's allele 1
#ima2p2 = df2$x2[df2$Parent2]) # Parent2's allele 2
out <- lapply(1:nmark, function(ind){
n <- nvar/2
transform(df2, ima1p1 = df2[, a[ind]][df$Parent1], # Parent 1's
allele 1
ima2p1 = df2[, b[ind]][df2$Parent1], # Parent 1's
allele 2
ima1p2 = df2[, a[ind]][df2$Parent2], # Parent 2's
allele 1
ima2p2 = df2[, a[ind]][df2$Parent2])} # Parent2's
allele 2
I could go further down because I had already an error ! I am particularly
confused how can apply the index in df2$Parent1 or df2$ parent2.
Please help.
Thank you;
Umesh R
_____
From: Umesh Rosyara [mailto:rosyar...@gmail.com]
Sent: Monday, February 28, 2011 8:01 AM
To: 'Dennis Murphy'
Cc: 'r-help@r-project.org'
Subject: stuk at another point: simple question
Dear R-community members.
I am really appreciate R-help group. Dennis has been extrremely helpful to
solve some of my questions. I am following Dennis recommendation in the
following email, yet I am stuck at another point (hope this will took me to
end of this project.
Ind <- c(1:5)
Parent1 <- c(NA,NA,1,1,3)
Parent2 <- c(NA,NA,2,2,4)
y <- c(6,5,8,10,7)
M1a <- c(1,2,1,1,1)
M1b <- c(1,2,2,2,1)
M2a <- c(3,3,1,1,3)
M2b <- c(1,1,3,3,3)
M3a <- c(4,4,4,4,4)
M3b <- c(4,4,1,1,4)
M4a <- c(1,4,4,1,4)
M4b <- c(4,4,4,4,4)
dataf <- data.frame (Ind, Parent1, Parent2, y, M1a, M1b,M2a,M2b,
M3a,M3b,M4a, M4b) # I have more than >1000 variables pair
# pair1 (M1a,M1b) pair2 (M2a, M2b), pair3 (M3a, M3b)...
df2 <- transform(dataf,m1ap1 = dataf$M1a[dataf$Parent1],
m1bp1 = dataf$M1b[dataf$Parent1],
m1ap2 = dataf$M1a[dataf$Parent2],
m1bp2 = dataf$M1b[dataf$Parent2])
# downstream calculations
hP1 <- ifelse(df2$m1ap1==df2$m1bp1,0,1)
hP2 <- ifelse(df2$m1bp2==df2$m1bp2,0,1)
t1 <- ifelse(df2$M1a==df2$m1ap1,1,0)
t2 <- ifelse(df2$M1b==df2$m1ap2,1,0)
C <- (hP1*(t1-0.25)+ hP2 *(t2-0.25))
yv <- df2$y
Cy <- C*yv
avgCy <- mean(Cy, na.rm=T)
avgCy # I want to store this value to new dataframe with first model i.e.
How can I loop the process to output the second pair( here M2a, M2b), third
pair (here M3a, M3b) to all pairs (I have more than 1000)
Mode1 avgCy
1 1.75 # from pair M1a and M1b
2 # from pair M2a and M2b
3 # from pair M3a and M3b
4 # from pair M4a and M4b
to the end of the file
Thank you in advance
Umesh R
_____
From: Dennis Murphy [mailto:djmu...@gmail.com]
Sent: Friday, February 18, 2011 12:28 AM
To: Umesh Rosyara
Cc: r-help@r-project.org
Subject: Re: [R] recoding a data in different way: please help
Hi:
This is as far as I could get:
df <- read.table(textConnection("
Individual Parent1 Parent2 mark1 mark2
1 0 0 12 11
2 0 0 11 22
3 0 0 13 22
4 0 0 13 11
5 1 2 11 12
6 1 2 12 12
7 3 4 11 12
8 3 4 13 12
9 1 4 11 12
10 1 4 11 12"), header = TRUE)
df2 <- transform(df, Parent1 = replace(Parent1, Parent1 == 0, NA),
Parent2 = replace(Parent2, Parent2 == 0, NA))
df2 <- transform(df2, imark1p1 = df2$mark1[df2$Parent1], # Parent 1's
mark1
imark1p2 = df2$mark1[df2$Parent2],
# Parent 2's mark1
imark2p1 = df2$mark2[df2$Parent1],
# Parent 1's mark2
imark2p2 = df2$mark2[df2$Parent2])
# Parent 2's mark2
I created df2 so as not to overwrite the original in case of a mistake. At
this point, you have several sets of vectors that you can compare; e.g.,
mark1 with imark1p1 and imark1p2. Like Josh, I couldn't make heads or tails
out of what these logical tests were meant to output, but perhaps this gives
you a broader template with which to work. At this point, you can probably
remove the rows corresponding to the parents. I believe ifelse() is your
friend here - it can perform logical tests in a vectorized fashion. As long
as the tests are consistent from one individual to the next, it's likely to
be an efficient route.
HTH,
Dennis
On Thu, Feb 17, 2011 at 6:21 PM, Umesh Rosyara <rosyar...@gmail.com> wrote:
Dear R users
The following question looks simple but I have spend alot of time to solve
it. I would highly appeciate your help.
I have following dataset from family dataset :
Here we have individuals and their two parents and their marker scores
(marker1, marker2,....and so on). 0 means that their parent information not
available.
Individual Parent1 Parent2 mark1 mark2
1 0 0 12 11
2 0 0 11 22
3 0 0 13 22
4 0 0 13 11
5 1 2 11 12
6 1 2 12 12
7 3 4 11 12
8 3 4 13 12
9 1 4 11 12
10 1 4 11 12
I want to recode mark1 and other mark2.....and so on column by looking
indvidual parent (Parent1 and Parent2).
For example
Take case of Individual 5, who's Parent 1 is 1 (has mark1 score 12) and
Parent 2 is 2 (has mark1 score 11). Individual 5 has mark1 score 11. Suppose
I have following condition to recode Individual 5's mark1 score:
For mark1 variable, If Parent1 score "11" and Parent2 score "22" and recode
indvidual 5's score, "12"=1, else 0
If Parent1 score "12" and Parent2 score
"22" and recode individual 5's score, "22"=1, "12"= 0.5, else 0
.........................more conditions
Similarly the pointer should move from individual 5 to n individuals at the
end of the file.
Thank you in advance
Umesh R
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