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gradlab / pcn_tet_susceptibility_gwas

Data and code for "Genome wide association studies define minimal set of loci for prediction of penicillin and tetracycline susceptibility in Neisseria gonorrhoeae"
MIT License
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Manhattan Plot - Unitigs Annotation Column Missing #1

Open isaaczhao23 opened 1 month ago

isaaczhao23 commented 1 month ago

The function to generate the Manhattan plot requires the annotation column from the unitigs dataset (data/gwas/tet/tet_unitig_annotated_WHO_N.txt) (column position 9). However, the dataset only has 8 columns, thus the annotation column is missing image

isaaczhao23 commented 1 month ago

This can be fixed by making a new column called "annotation" from "notes"

line 12: unitigs <- read_tsv("data/gwas/tet/tet_unitig_annotated_WHO_N.txt", col_names = c("unitig", "af", "filter_p", "lrt_p", "beta", "beta_std_err", "h2", "notes", "annotation")) %>% mutate(annotation = notes)

line 50: unitigs_pcn <- read_tsv("data/gwas/pcn/pcn_unitig_annotated_WHO_N.txt", col_names = c("unitig", "af", "filter_p", "lrt_p", "beta", "beta_std_err", "h2", "notes", "annotation")) %>% mutate(annotation = notes)