Description Usage Arguments Details Value
View source: R/process_mappings.R
find_peaks
Identifies QTL from GWAS mapping data set.
1 | find_peaks(processed_mapping_df, CI_size = 50, snp_grouping = 200)
|
processed_mapping_df |
The first element of the output list from the |
CI_size |
defines the size (in # SNPs) of confidence intervals. Default is 50 and is defined in more detail below. |
snp_grouping |
defines grouping of peaks. Defined further below, default is 200. |
This function identifies QTL by looking at SNPs above the bonferroni corrected p-value.
If only one SNP passed the significance cutoff, then the confidence interval is defined
as +/- CI_size
(number of SNPs; default 50) away from that SNP. If multiple SNPs
are above the cutoff, the function asks if SNPs are within an arbitrary number of SNPs away
snp_grouping
- default 200. If the significant SNPs are within this range, they are grouped into the same peak.
If they are greater than this distance, then the peaks are considered unique.
Outputs a two element list that contains. First element - data frame containing all identified intervals Second element - list containing one element for each interval
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