Example files for reproducing the R code.

[xie186]

Hi @myonaung,

Thank you for sharing the code.

In the two lines below, we do not see the corresponding files provided in the github link:

Naung-et-al-2021/Phasing_Haplotype/pf3k_antigen.Rmd

Line 68 in 89143c5

func_annotations <- readr::read_rds("pf3kv5_functional_annotations_filtered.rds")

Naung-et-al-2021/Phasing_Haplotype/pf3k_antigen.Rmd

Line 349 in 89143c5

cds_seq <- read.dna(paste0("ref", gene, ".1.fasta"), format="fasta") %>% as.character %>% as.vector %>% toupper

Could you please let us know what columns are included in pf3kv5_functional_annotations_filtered.rds and what are the *.1.fasta files? Thanks again!

[myonaung]

@xie186 , Thanks very much for your interest in our published manuscript. Please see example .rds file at
pf3kv5_functional_annotations_filtered_subset.csv.

*.1.fasta can be any reference file excluding intronic region.

Let me know if you have any further questions

[xie186]

Thank you so much for you help @myonaung !