Entering edit mode
6.0 years ago
paolo002
▴
160
Hi all
I have a data frame with various SNPs and other columns with some information and values such as the following:
SNP ID. location chromosome values column A. values column B
rs8662689 78654 1 0.6432 0.2458
rs753279 1009753 7 -1.6434 1.9876
rs4331780 2086433 22 4.521 -3.743
and so on...... ..... ......
I would like to standardise the values in column B. I understand I have to divide the column B in various frequency bins ( I have 20x10^6 rows so I guess I need to set a bin value by which to divide, for instance 1000). Then I would like to calculate the mean of each bin and the standard deviation and divide each value in column B by that particular mean and standard deviation calculated previously in each bin and create a new column. Anybody knows how to do this by a R code?
I have written something like this but it does not seem to work, might be wrong:
library(dplyr)
n_bins = 1000
outscore = df %>% mutate(bin=ntile(mean(df$valuesB),n_bins)) %>%
group_by(bin) %>% mutate(zscore=scale(mean()),outlier=abs(zscore)>1.7)
Any help highly appreciated. Thanks
for z score calculation, R has scale function.
Yes, I know, but if I apply only scale to the column it calculates the scores for each value of column B but it is not dividing by frequency bins
Not clear what you want to do, maybe provide example input data, and expected output? Also, this
ntile(mean(df$valuesB),n_bins)creates only 1 bin, and thisscale(mean())meant to bescale(mean(valuesB))?Apologies for the not so clear explanation Here is a sample of my data, first 20 rows:
I would like to standardise the values of the XPEHH column. I guess from what I understand I need to divide the values in bins and calculate the z-scores on the separate bins. So in this example for instance if I group by 10 bins I calculate the mean of the first 10 values and their standard deviation and calculate the z-score of those 10 SNPs based on the mean and SD previously calculated. The following is again done on the following 10 values/SNPs. Hope that is a bit clearer. Yes, I meant scale(mean(valuesB)) If I do only df$zscores<-scale(df$XPEHH) it calculates the zscore globally, I want to calculates the zscores on the separate bins.
Thank you very much, I think I can see this is most likely what I need because in the bin column it is grouping SNPs with similar values and then it calculates the zscore. Thanks a lot.
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