In roblanf/sangeranalyseR: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

`r if(!is.null(params$navigationAlignmentFN)){ "

SangerAlignment Level

" }`

SangerContig Level

SangerRead Level

library(sangeranalyseR)

Basic Information:

• Output Directory : r params$outputDir

cat("<li>**Input Source : **  <span><i>", params$SangerContig@inputSource, "</i></span></li>")
cat("<li>**Process Method : **  <span><i>", params$SangerContig@processMethod, "</i></span></li>")

if (params$SangerContig@inputSource == "ABIF" && !is.null(params$SangerContig@ABIF_Directory)) {
    cat("<li>**Input ABIF Directory : **  <span><i>", params$SangerContig@ABIF_Directory, "</i></span></li>")
} else if (params$SangerContig@inputSource == "FASTA" && !is.null(params$SangerContig@FASTA_File)){
    cat("<li>**Fasta File Name : **  <span><i>", params$SangerContig@FASTA_File, "</i></span></li>")
}

if (params$SangerContig@processMethod == "REGEX" && !is.null(params$SangerContig@REGEX_SuffixForward) && !is.null(params$SangerContig@REGEX_SuffixReverse)) {
      cat("<li>**Forward Reads Suffix Regex : **  <span><i>", params$SangerContig@REGEX_SuffixForward, "</i></span></li>")
      cat("<li>**Reverse Reads Suffix Regex : **  <span><i>", params$SangerContig@REGEX_SuffixReverse, "</i></span></li>")
} else if (params$SangerContig@processMethod == "CSV" && !is.null(params$SangerContig@CSV_NamesConversion)) {
        cat("<li>**Names Conversion CSV file : **  <span><i>", params$SangerContig@CSV_NamesConversion, "</i></span></li>")
} 

• Contig Name : r basename(params$SangerContig@contigName)
• Forward Read Number : r length(params$SangerContig@forwardReadList)
• Reverse Read Number : r length(params$SangerContig@reverseReadList)

---

'SangerContig' Input Parameters :

• Minimum Read Number : r params$SangerContig@minReadsNum
• Minimum Read Length : r params$SangerContig@minReadLength
• Minimum Fraction Call : r params$SangerContig@minFractionCall
• Maximum Fraction Lost : r params$SangerContig@maxFractionLost
• Accept Stop Codons : r params$SangerContig@acceptStopCodons
• Reading Frame : r params$SangerContig@readingFrame

---

Contig Sequence:

Primary Sequence

if (params$colors == "default") {
  A_color = "#1eff00"
  T_color = "#ff7a7a"
  C_color = "#7ac3ff"
  G_color = "#c9c9c9"
  unknown_color = "purple"
} else if (params$colors == "cb_friendly") {
  A_color = rgb(122, 122, 122, max = 255)
  T_color = rgb(199, 199, 199, max = 255)
  C_color = rgb(0, 114, 178, max = 255)
  G_color = rgb(213, 94, 0, max = 255)
  unknown_color = rgb(204, 121, 167, max = 255)
} else {
  A_color = colors[1]
  T_color = colors[2]
  C_color = colors[3]
  G_color = colors[4]
  unknown_color = colors[5]
}
contigSeq <- unlist(strsplit(as.character(params$SangerContig@contigSeq), ""))
contigSeqDF <- data.frame(t(data.frame(contigSeq)), stringsAsFactors = FALSE)
colnames(contigSeqDF) <- substr(colnames(contigSeqDF), 2, 100)
rownames(contigSeqDF) <- NULL
AstyleList <- SetCharStyleList(contigSeqDF, "A", A_color)
TstyleList <- SetCharStyleList(contigSeqDF, "T", T_color)
CstyleList <- SetCharStyleList(contigSeqDF, "C", C_color)
GstyleList <- SetCharStyleList(contigSeqDF, "G", G_color)
styleList <- c(AstyleList, TstyleList, CstyleList, GstyleList)
suppressWarnings(suppressMessages(
    excelTable(data = contigSeqDF, defaultColWidth = 30,
               editable = FALSE, rowResize = FALSE,
               columnResize = FALSE, allowInsertRow = FALSE,
               allowInsertColumn = FALSE, allowDeleteRow = FALSE,
               allowDeleteColumn = FALSE, allowRenameColumn = FALSE,
               style = styleList, loadingSpin = TRUE, autoWidth = FALSE)
))

--- # Reference Amino Sequence :

Genetic Code

wzxhzdk:3

Reference Amino Acid Sequence

wzxhzdk:4

--- # Contig Results:

Reads Alignment

wzxhzdk:5

Difference Data Frame

wzxhzdk:6

Distance Matrix

wzxhzdk:7

Dendrogram

wzxhzdk:8

wzxhzdk:9

Indels Data Frame

wzxhzdk:10

Stop Codons

wzxhzdk:11

Secondary Peak Data Frame

wzxhzdk:12

---

Forward Read Reports

wzxhzdk:13

wzxhzdk:14

---

Reverse Read Reports

wzxhzdk:15

wzxhzdk:16

---
`r if(!is.null(params$navigationAlignmentFN)){paste0('

Back to \'SangerAlignment Report\'')}`

roblanf/sangeranalyseR documentation built on April 15, 2024, 12:44 a.m.