how to read in saved scan1 output

[elsade...@gmail.com]

Hi, is there a way to read in a scan1 object saved as a .csv and convert it back to a scan1? I've tried to just read it using read.csv, but I get errors when using the maxlod or plot_scan1 function on the resulting data frame, presumably because it's the wrong class.

[Karl Broman]

Try class(myobject) <- c("scan1", "matrix")

karl

[elsade...@gmail.com]

This gives a scan1 object, but it's differently formatted than the original, and still doesn't work with the other functions.

starting with out, which is a scan1 of one phenotype (just as an example):

write.csv(out, "outtest.csv", row.names = F)
out2 <- read.csv("outtest.csv")
class(out2) <- c("scan1", "matrix")

Additional help appreciated, so I can plot my saved output!

[Dan Gatti]

I usually use saveRDS() and readRDS() with scan1 objects.  These write the data as compressed, binary objects. As long as you load the qtl2 library first, they should read in with the correct class type and you should be able to plot LOD curves directly.

 

Dan

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[Karl Broman]

The row names in a scan1 object are critical. They need to contain the marker names and are used to align the LOD scores with the map.

Like Dan, I'd use saveRDS() and readRDS() to save scan1 objects to a file. Alternatively, you can use save() and load().

But if you want to save the results as a CSV, you need to preserve the row names, and then you need to do a bit more work when reading it back in.

Here's an example:

library(qtl2)

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))

pr <- calc_genoprob(iron)

out <- scan1(pr, iron$pheno)

out <- scan1(pr, iron$pheno, Xcovar=get_x_covar(iron))

write.csv(out, "outtest.csv")

out2 <- read.csv("outtest.csv")

rownames(out2) <- out2[,1]

out2 <- as.matrix(out2[, -1])

plot_scan1(out2, iron$pmap)

karl