| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: DominoEffect |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Identification and Annotation of Protein Hotspot Residues |
| 4 |
-Version: 1.5.0 |
|
| 4 |
+Version: 1.5.1 |
|
| 5 | 5 |
Author: Marija Buljan and Peter Blattmann |
| 6 | 6 |
Maintainer: Marija Buljan <[email protected]>, |
| 7 | 7 |
Peter Blattmann <[email protected]> |
| ... | ... |
@@ -12,9 +12,9 @@ GPo_of_hotspots <- function(hotspot_mutations){
|
| 12 | 12 |
prot_residue_info <- data.frame(do.call('rbind',
|
| 13 | 13 |
strsplit(as.character(hotspots_genomic_info$AA_position), |
| 14 | 14 |
'-',fixed=TRUE))) |
| 15 |
- chr_info <- paste ("chr", hotspots_genomic_info$Genomic_coordinate, "-",
|
|
| 16 |
- coordinates_sep$X2, sep = "") |
|
| 17 |
- hotspots_GPo <- GPos(chr_info) |
|
| 15 |
+ chr_info = paste("chr", coordinates_sep$X1)
|
|
| 16 |
+ position_on_chr = coordinates_sep$X2 |
|
| 17 |
+ hotspots_GPo <- GPos(seqnames=chr_info, pos= position_on_chr, stitch=FALSE) |
|
| 18 | 18 |
|
| 19 | 19 |
GenomicRanges::mcols(hotspots_GPo)$REF_NT <- as.character(hotspots_genomic_info$Original_base) |
| 20 | 20 |
GenomicRanges::mcols(hotspots_GPo)$MUT_NT <- as.character(hotspots_genomic_info$Mutated_base) |
| ... | ... |
@@ -110,11 +110,10 @@ identify_hotspots <- function(mutation_dataset, gene_data , snp_data, |
| 110 | 110 |
if(length(snp_data) > 0){
|
| 111 | 111 |
### convert data.frame into GPos |
| 112 | 112 |
if(class(snp_data) == "data.frame"){
|
| 113 |
- chr_info <- paste("chr", snp_data$Chr_name,":",
|
|
| 114 |
- snp_data$Position_on_chr, "-", |
|
| 115 |
- snp_data$Position_on_chr, sep = "") |
|
| 113 |
+ chr_info <- paste("chr", snp_data$Chr_name)
|
|
| 116 | 114 |
freq_info <- snp_data$Minor_allele_freq |
| 117 |
- snp_data <- GPos(chr_info) |
|
| 115 |
+ position_on_chr <- snp_data$Position_on_chr |
|
| 116 |
+ snp_data <- GPos(seqnames=chr_info, pos= position_on_chr, stitch=FALSE) |
|
| 118 | 117 |
GenomicRanges::mcols(snp_data)$Minor_allele_freq <- freq_info |
| 119 | 118 |
} |
| 120 | 119 |
|
| ... | ... |
@@ -129,9 +128,9 @@ identify_hotspots <- function(mutation_dataset, gene_data , snp_data, |
| 129 | 128 |
snps <- variant_start == variant_end |
| 130 | 129 |
chromosomes <- as.character(seqnames(coords_common_vars[snps])) |
| 131 | 130 |
freq_info <- vcf_table[common_vars[snps],"LDAF"] |
| 132 |
- chr_info <- paste("chr", chromosomes,":",
|
|
| 133 |
- variant_start[snps], "-", variant_end[snps], sep = "") |
|
| 134 |
- snp_data <- GPos(chr_info) |
|
| 131 |
+ chr_info = paste("chr", chromosomes)
|
|
| 132 |
+ position_on_chr = variant_start[snps] |
|
| 133 |
+ snp_data <- GPos(seqnames=chr_info, pos= position_on_chr, stitch=FALSE) |
|
| 135 | 134 |
GenomicRanges::mcols(snp_data)$Minor_allele_freq <- freq_info |
| 136 | 135 |
} |
| 137 | 136 |
|
| ... | ... |
@@ -1,3 +1,25 @@ |
| 1 |
+CHANGES IN VERSION 1.5.1 |
|
| 2 |
+------------------------- |
|
| 3 |
+UDPATE |
|
| 4 |
+ |
|
| 5 |
+ o Adapt to new GenomicRanges::GPo function |
|
| 6 |
+ |
|
| 7 |
+ |
|
| 8 |
+ |
|
| 9 |
+CHANGES IN VERSION 1.5.0 |
|
| 10 |
+------------------------- |
|
| 11 |
+UDPATE |
|
| 12 |
+ |
|
| 13 |
+ o DominoEffect BioC 3.10 development version |
|
| 14 |
+ |
|
| 15 |
+ |
|
| 16 |
+CHANGES IN VERSION 1.4.0 |
|
| 17 |
+------------------------- |
|
| 18 |
+UDPATE |
|
| 19 |
+ |
|
| 20 |
+ o DominoEffect BioC 3.9 release version |
|
| 21 |
+ |
|
| 22 |
+ |
|
| 1 | 23 |
CHANGES IN VERSION 1.3.1 |
| 2 | 24 |
------------------------- |
| 3 | 25 |
UDPATE |
