plotting SEs against allele frequency in R
Dear all,
I have a dataset with two Standard errors from different experiments of *GWAS. And trying to see how it varies against the allele frequency. This to discard any outliers from the following analysis.
so the dataset looks like
$maf $SE1 $SE2
0.01 0.356 0.348
0.05 0.456 0.245
..... ....... ........
I managed to find a plot that matches the description. I have tried the plot in the base graphics of . is there any package that can provide such plots. Any suggestions will be of great help. Thanks so much
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iphoenix2100 •
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Are you willing to use the ggplot2 package? That would make your life easier and using that is VERY common.
Do you have the data available to produce the plot? The example data you have show only MAF and SE? Are you asking how to make a plot or how to get the odds ratio and risk allele frequency? What do you want the colors to represent?