error: fewer than one row in the data in runGprimeAnalysis about qtlseqr

[bmansfeld]

Hi,
You are showing me the head(df) but running the command on df_filt.
df_filt <- runGprimeAnalysis(SNPset = df_filt, windowSize = 1e6, outlierFilter = "deltaSNP")
Did you filter snps already?
How many rows in the df_filt data frame? Just based on the error msg it seems that the df_filt is empty?
Or maybe one of the Chrms is empty.
Something is strange with the data.
Ben

[cjchen5]

Hi Ben,
Thank you! I guess one of the Chrms is empty after filtering. I will check it later.
BTW, I have another question for Gprime plot. The deltaSNP plot from same data is continuous but Gprime plot have a weird gap near the peak. Could you tell me what might cause the gap in Gprime plot?

[bmansfeld]

Hi,
The default y axis limits are -0.6 to 0.6, you have a nice peak there going past that range so it's getting cut off. You are probably also getting a warning message about values not being mapped.
To remedy this you should add + ylim(-1,1) or some other range after your plotQTLStats() function.
Ben

[cjchen5]

Thanks! But when I change my plot code to:
plotQTLStats(SNPset = df_filt, var = "deltaSNP", plotIntervals = TRUE, + ylim(-1,1))
Error in ylim(-1, 1) : could not find function "ylim"
Could you please tell me more detail of add + ylim(-1,1)?
Thank you very much!

[bmansfeld]

The function is a wrapper for ggplot therefore you need to add + ylim() after the function.
I.e. plotQTLStats(....) + ylim(..)
Look at the ggplot package to understand more.
Ben

[cjchen5]

Thank you so much!
When I library("ggplot2") first and then plotQTLStats(....) + ylim(..) it works.