hendriau
commented
3 years ago Thank you for your question and interest in ProxECAT.
Proxecat can take vectors. Thus, if you have a dataframe where you have the rows equal to the genes of interest and columns for the number of functional variants and synonymous variants by case and control status, you can put the vectors into proxecat. Proxecat will output a vector of the test statistics and p-values.
A toy example is below:
temp<-data.frame(x1=c(1:10), x2=c(2:11), x3=c(3:12), x4=c(4:13)) proxecat::proxecat(temp$x1, temp$x2, temp$x3, temp$x4)
I hope this helps! Audrey
I am on sabbatical through the 2021-2022 AY and thus may be slower to respond. Audrey E. Hendricks, Ph.D. Associate Professor of Statistics Department of Mathematical and Statistical Sciences University of Colorado Denver | Anschutz Medical Campus Student Commons Building (SCB, AB-1; room 4217) @.**@.> audreyhendricks.comhttp://www.math.ucdenver.edu/~ahendricks/ @hendricks_ae pronouns: she/her/hers
From: Baiba Alksere @.> Date: Monday, September 27, 2021 at 12:33 PM To: hendriau/ProxECAT @.> Cc: Subscribed @.***> Subject: [hendriau/ProxECAT] input many gene regions (#3) [External Email - Use Caution]
Hello, So I have the script for getting both synonymous and misense variants fom VCF file. Now I wonder, how to input these results from many genes into ProxECAT vector? How should input file look like? The sample given in README shows only option for one gene region.
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Hello, So I have the script for getting both synonymous and misense variants fom VCF file. Now I wonder, how to input these results from many genes into ProxECAT vector? How should input file look like? The sample given in README shows only option for one gene region.