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annotations_clubfoot.Rmd
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---
title: "annotations_SV"
author: "Dominika Kresa"
date: "25 04 2021"
output: html_document
---
```{r}
suppressMessages(library(dplyr))
suppressMessages(library(tidyr))
suppressMessages(library("writexl"))
annotations_SV <-
read.delim(file = "/home/dominika_kresa/old_clubfoot.merged.annotated.bed",
sep = "\t",
stringsAsFactors = F)
```
```{r}
annotations_SV_GT_3 <- annotations_SV %>% select(
seqnames,
start,
end,
change_type,
QUAL_lumpy,
III20_consensus_GT,
III21_consensus_GT,
IV33_consensus_GT,
V14_consensus_GT,
lumpy_site_info,
ncbiRefSeqCurated,
geneHancerGenesTssDoubleElite,
Num_exons,
DGV,
seqnames.1,
GNOMAD,
link,
score,
score_gene,
OMIM_green,
OMIM_yellow
) %>% filter(
!change_type == "BND",
score > 0,
III21_consensus_GT == "0/0",
!III20_consensus_GT == "0/0",
!IV33_consensus_GT == "0/0",
!V14_consensus_GT == "0/0"
) %>% arrange(desc(score))
View(annotations_SV_GT_3)
```
```{r}
annotations_SV_GT_2 <- annotations_SV %>% select(
seqnames,
start,
end,
change_type,
QUAL_lumpy,
III20_consensus_GT,
III21_consensus_GT,
IV33_consensus_GT,
V14_consensus_GT,
lumpy_site_info,
ncbiRefSeqCurated,
geneHancerGenesTssDoubleElite,
Num_exons,
DGV,
seqnames.1,
GNOMAD,
link,
score,
score_gene,
OMIM_green,
OMIM_yellow
) %>% filter(
!change_type == "BND",
score > 0,
III21_consensus_GT == "0/0",
III20_consensus_GT == "0/0" &
!IV33_consensus_GT == "0/0" &
!V14_consensus_GT == "0/0" |
!III20_consensus_GT == "0/0" &
IV33_consensus_GT == "0/0" &
!V14_consensus_GT == "0/0" |
!III20_consensus_GT == "0/0" &
!IV33_consensus_GT == "0/0" & V14_consensus_GT == "0/0"
) %>% arrange(desc(score))
View(annotations_SV_GT_2)
```
```{r}
annotations_SV_GT_1 <- annotations_SV %>% select(
seqnames,
start,
end,
change_type,
QUAL_lumpy,
III20_consensus_GT,
III21_consensus_GT,
IV33_consensus_GT,
V14_consensus_GT,
lumpy_site_info,
ncbiRefSeqCurated,
geneHancerGenesTssDoubleElite,
Num_exons,
DGV,
seqnames.1,
GNOMAD,
link,
score,
score_gene,
OMIM_green,
OMIM_yellow
) %>% filter(
!change_type == "BND",
score > 0,
III21_consensus_GT == "0/0",
III20_consensus_GT == "0/0" &
IV33_consensus_GT == "0/0" &
!V14_consensus_GT == "0/0" |
!III20_consensus_GT == "0/0" &
IV33_consensus_GT == "0/0" &
V14_consensus_GT == "0/0" |
III20_consensus_GT == "0/0" &
!IV33_consensus_GT == "0/0" & V14_consensus_GT == "0/0"
) %>% arrange(desc(score))
View(annotations_SV_GT_1)
```
```{r}
annotations_SV_m1 <-
rbind(annotations_SV_GT_3,
annotations_SV_GT_2,
annotations_SV_GT_1)
annotations_SV_m2 <-
annotations_SV_m1 %>% unite("POS", seqnames:start, sep = ":", remove = TRUE)
annotations_SV_merged <-
annotations_SV_m2 %>% unite("chr:start-end", POS:end, sep = "-", remove = TRUE)
View(annotations_SV_merged)
```
```{r}
write_xlsx(annotations_SV_merged,
"/home/dominika_kresa//annotations_SV_merged.xlsx")
```