plotting SEs against allele frequency in R

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9.9 years ago

iphoenix2100 ▴ 50

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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r • 3.1k views

ADD COMMENT • link updated 2.7 years ago by Ram 44k • written 9.9 years ago by iphoenix2100 ▴ 50

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Entering edit mode

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?

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 9.9 years ago by Sean Davis 27k

0

Entering edit mode

Are you willing to use the ggplot2 package? That would make your life easier and using that is VERY common.

ADD REPLY • link updated 2.7 years ago by Ram 44k • written 9.9 years ago by Devon Ryan 104k

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