| Type: | Package |
| Title: | CRISPR-Based Salmonella Enterica Serotype Analyzer |
| Version: | 1.2.0 |
| Description: | Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Serotype identification is the most commonly used typing method to characterize Salmonella isolates. However, experimental serotyping needs great cost on manpower and resources. Recently, we found that the newly incorporated spacer in the clustered regularly interspaced short palindromic repeat (CRISPR) could serve as an effective marker for typing of Salmonella. It was further revealed by Li et. al (2014) <doi:10.1128/JCM.00696-14> that recognized types based on the combination of two newly incorporated spacer in both CRISPR loci showed high accordance with serotypes. Here, we developed an R package 'CSESA' to predict the serotype based on this finding. Considering it’s time saving and of high accuracy, we recommend to predict the serotypes of unknown Salmonella isolates using 'CSESA' before doing the traditional serotyping. |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| Encoding: | UTF-8 |
| LazyData: | true |
| RoxygenNote: | 6.0.1 |
| Suggests: | testthat |
| Imports: | Biostrings |
| NeedsCompilation: | no |
| Packaged: | 2019-03-02 11:48:19 UTC; Xia |
| Author: | Xia Zhang [aut, cre], Lang Yang [aut] |
| Maintainer: | Xia Zhang <zhangxia9403@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2019-03-03 16:40:02 UTC |
CSESA (CRISPR-based Salmonella enterica Serotype Analyzer).
Description
The main function in CSESA package.
Usage
CSESA(in.file1 = NULL, in.file2 = NULL, out.file = NULL,
method = c("PCR", "WGS"))
Arguments
in.file1 |
The first input file, the default value is NULL. |
in.file2 |
The second input file (optional), the default value is NULL. |
out.file |
Into which results will be saved if this value is set. Otherwise results will be displayed on the screen. |
method |
The method to handle the input file(s), which can be set as "PCR" or "WGS". Choose "PCR" if the CRISPR sequence(s) from PCR amplification is entered, and choose "WGS" when entering the whole genome assembly of a Salmonella isolate. |
Note
If you use the "WGS" method, please make sure you have installed the BLAST software and included it within the working path.
Examples
CSESA(system.file("extdata", "sequence_CRIPSR1.fasta", package = "CSESA"),
system.file("extdata", "sequence_CRIPSR2.fasta", package = "CSESA"), method = "PCR")
CSESA(system.file("extdata", "sequence_CRIPSR1.fasta", package = "CSESA"), method = "PCR")
CSESA(system.file("extdata", "Salmonella_whole_genome_assembly.fasta",
package = "CSESA"), method = "WGS")
Find the serotype based on the analysis of the new spacers.
Description
Find the serotype based on the analysis of the new spacers.
Usage
FindSerotype(csesa1 = NA, csesa2 = NA)
Arguments
csesa1 |
The new spacer of the first sequence. |
csesa2 |
The new spacer of the second sequence. |
Value
The data frame which represents the serotype.
Get the new spacers from the molecular sequence and its reverse complement.
Description
Get the new spacers from the molecular sequence and its reverse complement.
Usage
GetAllNewSpacers(molecular.seq = NULL)
Arguments
molecular.seq |
The molecular sequence. |
Value
The vector of the new spacers, which is extracted from the molecular sequence and its reverse complement.
Note
If there doesn't exist any new spacer, the function would return NA.
Get the new spacer from the molecular sequence.
Description
Get the new spacer from the molecular sequence.
Usage
GetNewSpacer(molecular.seq = NULL)
Arguments
molecular.seq |
The molecular sequence. |
Value
The new spacer sequence as a string.
Examples
GetNewSpacer("AGAGGCGGACCGAAAAACCGTTTTCAGCCAACGTAT")
Get the new spacer from the molecular sequence and map it to the code.
Description
Get the new spacer from the molecular sequence and map it to the code.
Usage
GetNewSpacerCode(molecular.seq = NULL)
Arguments
molecular.seq |
The molecular sequence. |
Value
The new spacer code as a string.
Return the reverse complement of the sequence.
Description
Return the reverse complement of the sequence.
Usage
GetReverseComplement(x)
Arguments
x |
The input sequence. |
Value
The reverse complement sequence as a string.
Get the information string from the CSESA s3 object.
Description
Get the information string from the CSESA s3 object.
Usage
GetStr(csesa)
Arguments
csesa |
The S3 object CSESA. |
Value
The string record the newly spacers and serotype information.
Get the CSESA obeject through the two sequence.
Description
Get the CSESA obeject through the two sequence.
Usage
PCR(seq1, seq2, out.file)
Arguments
seq1 |
The first DNA sequence. |
seq2 |
The second DNA sequence. |
out.file |
Into which results will be saved if this value is set. Otherwise results will be displayed on the screen. |
Read the three types of input file.
Description
Read the three types of input file.
Usage
ReadInFile(file.name)
Arguments
file.name |
The input file name. |
Value
The molecular sequence as a string.
Find the serotype based on the analysis of the new spacers.
Description
Find the serotype based on the analysis of the new spacers.
Usage
WGS(file)
Arguments
file |
The input fasta file. |
Value
The two DNA molecular sequence.