[R] lodplot help

Al-Sabban, Shaza shaza.al-sabban at kcl.ac.uk
Wed Aug 24 19:28:42 CEST 2011


I have a data frame (narrow) with 431 rows and 6 columns containing information on chromosome, position, lod1, lod2, lod3, lod4, looking like this:

> narrow
   chr     pos   lod1   lod2   lod3   lod4
1     1   3.456 -0.025 -0.003 -0.209 -0.057
2     1   5.697 -0.029 -0.005 -0.200 -0.058
3     1   8.434 -0.049 -0.012 -0.247 -0.092
4     1   9.466 -0.074 -0.025 -0.300 -0.136
5     1   9.706 -0.074 -0.025 -0.298 -0.134
6     1  12.022 -0.067 -0.018 -0.280 -0.112
7     1  13.031 -0.061 -0.015 -0.268 -0.099
8     1  13.050 -0.061 -0.015 -0.268 -0.099
9     1  13.719 -0.055 -0.012 -0.252 -0.090


I am trying to plot the positions vs. scores using:

chromosome.viewlinkage (narrow, chrom=1, type="layout", statistic = "lod", with.X= TRUE, min.sat= -2, max.stat= 4, pheno.names = NULL, units = "cM", col =1:6, ltyp= 1, lwd = 2, chromosome.cex= 0.9)

or 

plot.scan  (narrow, chrom=1, type="layout", statistic = "lod", with.X= TRUE, min.sat= -2, max.stat= 4, pheno.names = NULL, units = "cM", col =1:6, ltyp= 1, lwd = 2, chromosome.cex= 0.9)

I get this error message: Error in if (length(col) < ncol(stat)) { : argument is of length zero.

Can you help me understand what I'm doing wrong? 

Thanks 
Shaza



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