Mapping in R/qtl

[Mohamed ElSoda]

Dear Karl,

I am using r/qtl to make a map for Brassica F7 RIL population. It is recognized as F2 "I think that should be ok?".

I used this script

Map <- read.cross("csv", "M:/R-qtl", "Map.csv", na.strings="na",genotypes=c("a","h","b"),alleles=c("a","b"), estimate.map=FALSE),   but I got this

warnning message 

In summary.cross(cross) :
    Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
    (Perhaps it is in basepairs?)

 I tried your reply to a previouse question by using (estimate.map, replace.map), but it didn't help.

Any advice?

 

Best regards,

Mohamed El-Soda,

Wageningen University, P.O. Box 309
6700 AH Wageningen
The Netherlands

 

[Karl Broman]

On May 13, 2011, at 5:54 AM, Mohamed ElSoda <elsoda....@gmail.com> wrote:

Dear Karl,

I am using r/qtl to make a map for Brassica F7 RIL population. It is recognized as F2 "I think that should be ok?".

I think no; you want to use convert2riself() to convert to cross type "riself". This will also drop het genotypes.

I used this script

Map <- read.cross("csv", "M:/R-qtl", "Map.csv", na.strings="na",genotypes=c("a","h","b"),alleles=c("a","b"), estimate.map=FALSE),   but I got this

warnning message 

In summary.cross(cross) :
    Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
    (Perhaps it is in basepairs?)

 I tried your reply to a previouse question by using (estimate.map, replace.map), but it didn't help.

Any advice?

In what way did it not work?  An error message?  

It may be that there are problem markers that are leading to big gaps in the map and need to be removed.

karl

[Mohamed ElSoda]

Dear Karl,

 

I am trying to get a heatmap using LOD scores.

I am using these scripts

 

x <- read.csv("bath")

row.names(x) <- x$Name

x<- x[,4:20] 

x_matrix <- data.matrix(x)

x_matrix <- t(x)

heatmap(as.matrix(x_matrix,nrow(x_matrix),ncol(x_matrix)),Colv=NA)

1-How can I set colours based on LOD scores (-6 to -4 = green), (-4 to -2 blue), (-2 to 2 = white), (2 to 4 = yellow), (4 to 6 = red)?

2- How to put a bar with colour scale?

 

Thanks in advance,

 

Mohamed

 

[Karl Broman]

Your question isn't related to R/qtl, but I'll attempt to answer it anyway.

I've never used the function heatmap(), but I expect it's similar to image(), for which you'd specify colors with the argument 'col' and intervals with 'breaks', like the following:

x <- matrix(runif(100, -6, 6), ncol=10)
colorpal <- c("green","blue","white","yellow","red")
brks <- c(-6, -4, -2, 2, 4, 6)
image(x, col=colorpal, breaks=brks)

To get a color scale, I've generally used layout() to create two side-by-sdie

layout(cbind(1,2), width=c(6,1))

colorpal <- c("green","blue","white","yellow","red")
brks <- c(-6, -4, -2, 2, 4, 6)
image(x, col=colorpal, breaks=brks)

v <- seq(-6, 6, length=251)
image(1, v, matrix(v, nrow=1), col=colorpal, breaks=brks, ylab="", xaxt="n", xlab="")

karl

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