AIRs Ref Manual
User Manual: Pdf
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Package ‘AIRs’
February 6, 2018
Type Package
Title Analyzer of Integrated Regions
Version 0.99.0
Date 2018-02-06
Author@R c( person(``Min-Jeong'', ``Baek'', email =
``mjbaek16@korea.ac.kr'', role = c(``aut'', ``cre'')),
person(``In-Geol'', ``Choi'', email = ``igchoi@korea.ac.kr'', role =
c(``aut'')) )
Author Min-Jeong Baek [aut, cre],
In-Geol Choi [aut]
Maintainer Computational & Synthetic Biology Lab <igchoi@korea.ac.kr>
Description This package was developed for analysis of regions where viral vectors are integrated.
Find the location of integrated regions and analyze whether it is associated with important ge-
nomic factors.
Finally, user can conduct random analysis based on the results of the previous analysis.
Depends R (>= 3.2.5)
Imports data.table (>= 1.10.4), ggbio (>= 1.18.5), ggplot2 (>= 2.2.1),
GenomeInfoDb (>= 1.6.3), GenomicRanges (>= 1.22.4), grDevices
(>= 3.2.5), graphics (>= 3.2.5), IRanges (>= 2.4.8), seqinr (>=
3.3), stats (>= 3.2.5), stringr (>= 1.2.0), S4Vectors (>=
0.8.11), utils (>= 3.2.5)
License GPL (>= 2)
Encoding UTF-8
LazyData true
RoxygenNote 6.0.1
Rtopics documented:
canine............................................ 2
chicken ........................................... 2
distribution ......................................... 3
1
2chicken
drawingIdeo......................................... 4
extractFeatures ....................................... 5
FASTAinfo ......................................... 6
findHits ........................................... 6
human............................................ 7
makeHitTable........................................ 8
monkey ........................................... 9
mouse............................................ 9
random ........................................... 10
readCpGdb ......................................... 11
readGFF........................................... 11
readRepeatdb ........................................ 12
readTSSdb.......................................... 12
Index 14
canine Refseq & UCSC chromosome id list - Canine
Description
Data is made from target FASTA file from NCBI Refseq and UCSC genome browser database.
Usage
data(canine)
Format
An object of class data.frame with 40 rows and 2 columns.
Examples
data(canine)
chicken Refseq & UCSC chromosome id list - Chicken
Description
Data is made from target FASTA file from NCBI Refseq and UCSC genome browser database.
Usage
data(chicken)
distribution 3
Format
An object of class data.frame with 8064 rows and 2 columns.
Examples
data(chicken)
distribution Functions for distribution analysis
Description
This function is for distribution analysis. Outputs are two kinds of histogram, drawing frequency
and density, and they are saved in outputpath. Plus, Each of data is saved in a data frame format
variable.
Usage
distribution(rawHitTable, annoHitTable, annotTableType, isHuman = FALSE,
featureTable, interval = 2, outputpath = getwd())
Arguments
rawHitTable Data frame of BLAST result (from makeHitTable_output$rawHits).
annoHitTable Data frame of annotated hits (from makeHitTable_output$annoHits).
annotTableType Choose one of genetical features such as gene, cpg, repeat, tss.
isHuman If target genome is human, enter TRUE. Default is FALSE.
featureTable Data frame of annotation databases.
interval Interval of distribution graph. User can choose 2kb or 5kb. Default is 2kb.
outputpath Full path of output file located (Except for file name). Default is working direc-
tory.
Format
Output format is a list :
overlaps A data table which consists of hits which have identities more than 95.
histdata A data table annotated form.
See Also
findHits
makeHitTable
Examples
distribution(hitset$rawHits, hitset$annotHits, annotTableType = cpg, featureTable = cpgdb,
interval = 2, outputpath = ~/test)
4drawingIdeo
drawingIdeo Function for drawing an ideogram plot
Description
This function makes an ideogram of NCBI Refseq chromosomes. An Ideogram image is saved in
the output folder.
Usage
drawingIdeo(regions, genes, rawHitTable, blastdb = "ncbi", chridTable,
outputpath = getwd())
Arguments
regions Data frame from NCBI Refseq annotation file (from extractFeatures_output$regions).
genes Data frame from annotation database file. (from extractFeatures_output$genes).
rawHitTable Data frame of BLAST result (from makeHitTable_output$rawHits).
blastdb Used sequence data for running BLASTm. User can choose ncbi and ucsc.
Default is ncbi.
chridTable A Data frame from package’s chrid datasets.
outputpath Full path of output file located (Except for file name). Default is working direc-
tory.
See Also
findHits
makeHitTable
extractFeatures
Examples
drawingIdeo(anno$region, anno$genes, hitset$rawHits, blastdb = ncbi, chicken, outputpath = ~/test)
extractFeatures 5
extractFeatures Function for making various type data table from NCBI Refseq anno-
tation file.
Description
This function makes data table include NCBI annotation features for searching hits’ information.
Before use this function, user should generate a data frame of gff file using by readGFF. Outputs
are 4 data frames about region, genes, transcripts and extra features. Especially, transcript data of
output is used for transcription start site analysis of not human and mouse.
Usage
extractFeatures(gff)
Arguments
gff A Data frame of GFF file.
Format
Output format is a list :
region A data table which consists of hits which have ’Region’ feature.
genes A data table which consists of hits which have ’Gene’ feature.
transcripts A data table which consists of hits which have ’Transcript’ or ’RNA’ features.
etc A data table which consists of hits which are not included previous sets.
See Also
readGFF
drawingIdeo
Examples
extractFeatures(gff)
6findHits
FASTAinfo Function for profiling FASTA file
Description
It is a function that displays sequence information in a fasta file.
Usage
FASTAinfo(inputpath)
Arguments
inputpath Full path of input file (FASTA format).
Format
Output is a data frame with 4 columns :
num The number of sequence in this file.
avr The average length of sequences in this file.
min The minimum value of sequence length.
max The maximum value of sequence length.
Examples
FASTAinfo(inputpath = ~/test/chicken.fna)
findHits Function for finding location of integration sites
Description
This function allows you to run CD-HIT-EST to reduce redundants and nucleotide BLAST for
searching integrated sites. For using this function, CD-HIT-EST and BLASTn is already installed.
Usage
findHits(inputfile, outputpath = getwd(), cdhitpath, blastnpath, blastdbpath,
btask = "megablast", thread = 1)
human 7
Arguments
inputfile Full path of sequence file (FASTA format).
outputpath Full path of output file located (Except for file name). Default is working direc-
tory.
cdhitpath Full path of CD-HIT-EST installed.
blastnpath Full path of BLASTn installed.
blastdbpath Full path of blastdb saved.
btask Choose a task between blastn and megablast. Default is megablast.
thread The number of core in your server for running BLASTn. Default is 1.
See Also
makeHitTable
distribution
random
drawingIdeo
Examples
findHits(inputfile = ~/test/chicken.fna, outputpath = ~/test,
cdhitpath = /csbl_local/tools/ngs/cd-hit-v4.6.6-2016-0711/cd-hit-est,
blastnpath = /csbl_local/tools/ngs/ncbi-blast-2.5.0+/bin/blastn,
blastdbpath = /home/shiny/irahome/db/chicken.fna, btask = megablast, thread = 4)
human Refseq & UCSC chromosome id list - Human
Description
Data is made from target FASTA file from NCBI Refseq and UCSC genome browser database.
Usage
data(human)
Format
An object of class data.frame with 328 rows and 2 columns.
Examples
data(human)
8makeHitTable
makeHitTable Function for making hit table about integrated regions into genomic
factors.
Description
This function selects hits integrated into genomic factors and these are from BLAST result file.
User can control minimum value of identities.
Usage
makeHitTable(inputdata, inputformat = "dataframe", ident_value = 95,
chridTable, annotTableType, featureTable)
Arguments
inputdata Full path of BLAST file (TBL format) or Data from findHits function (Dataframe).
inputformat Format of input data. User can choose one The user selects one of tbl and
dataframe. Default is dataframe.
ident_value Number of identities to filter out blast hits. Default is 95.
chridTable A Data frame from package’s chrid datasets.
annotTableType Choose one of genetical features such as gene, cpg, repeat, tss. If you are run-
ning tss annotation, you can only use it for non-human sequence analysis.
featureTable A Data frame from annotation databases.
Format
Output format is a list :
rawHits A data table which consists of hits which have identities more than specific value.
annoHits A data table annotated form.
multiHits A data table showed multihits.
See Also
extractFeatures
findHits
GenomicRanges
Examples
makeHitTable(inputdata = ~/test/blastn_result/chicken.tbl, inputformat = tbl, chridTable = chicken,
annotTableType = cpg, featureTable = cpgdb)
monkey 9
monkey Refseq & UCSC chromosome id list - Monkey
Description
Data is made from target FASTA file from NCBI Refseq and UCSC genome browser database.
Usage
data(monkey)
Format
An object of class data.frame with 572 rows and 2 columns.
Examples
data(monkey)
mouse Refseq & UCSC chromosome id list - Mouse
Description
Data is made from target FASTA file from NCBI Refseq and UCSC genome browser database.
Usage
data(mouse)
Format
An object of class data.frame with 44 rows and 2 columns.
Examples
data(mouse)
10 random
random Function for random analysis
Description
This function generates random samples and do chi-square test to see similarity. By this function,
you can make random distribution graph and chi-square statistic values.
Usage
random(overlapTable, rawHitTable, annoHitTable, histdata, featureTable,
interval = 2, samplenum = 1e+05, outputpath = getwd())
Arguments
overlapTable Data frame of findOverlaps output (from distribution_output$overlaps).
rawHitTable Data frame of BLAST result (from makeHitTable_output$rawHits).
annoHitTable Data frame of annotated hits (from makeHitTable_output$annoHits).
histdata Data table of distribution (from distribution_output$histdata).
featureTable Data frame of annotation databases.
interval Interval of distribution graph. User can choose 2kb or 5kb. Default is 2kb.
samplenum The number of samples in random set. Default value is 100000.
outputpath Full path of output file located (Except for file name). Default is working direc-
tory.
Format
Output format is a list :
random A random set.
chitable A data table that shows chitest result.
chiresult Summary of chi-squre test(by chisq.test()).
See Also
findHits
makeHitTable
distribution
chisq.test
Examples
random(overlapTable = distr$overlaps, rawHitTable = hitset$rawHits, annoHitTable = hitset$annotHits,
histdata = distr$histdata, featureTable = cpgdb, samplenum = 100000, outputpath = ~/test)
readCpGdb 11
readCpGdb Function for converting annotation file from UCSC to specific data
frame
Description
This function allows you to converting CpG site database file (text file type) to data frame for
analysis. User can download CpG site database file from UCSC genome browser.
Usage
readCpGdb(cpgfile, select = TRUE)
Arguments
cpgfile Full path of CpG site database file(text file format) from UCSC genome browser.
select If you want to include small size (<300bps) CpG sites in output, that should be
FALSE. TRUE is counterpart of that. Default is TRUE.
Examples
readCpGdb(cpgfile = ~/test/chicken_raw.cpg, select = FALSE)
readGFF Function for reading GFF file
Description
This function allows you to converting a gff file to data frame for analysis. User can download GFF
files from NCBI Refseq. Before using extractFeatures function, you should run this function.
Usage
readGFF(gffFile, nrows = -1)
Arguments
gffFile Full path of target’s annotation file (GFF format).
nrows Do not modify negative value of this.
See Also
extractFeatures
Examples
readGFF(gffFile = ~/test/chicken.gff)
12 readTSSdb
readRepeatdb Function for converting annotation file from UCSC to specific data
frame
Description
This function allows you to converting repeat database file (text file type) to data frame for analysis.
User can download repeat database file from UCSC genome browser.
Usage
readRepeatdb(repeatfile, includeSimpleRepeats = FALSE,
includeUnknownClass = FALSE)
Arguments
repeatfile Full path of repeat database file(text file format) from UCSC genome browser.
includeSimpleRepeats
If you want to include simple repeats in output, that should be TRUE. FALSE is
counterpart of that. Default is FALSE.
includeUnknownClass
If you want to include repeats that are included in unknown class, that should be
TRUE. FALSE is counterpart of that. Default is FALSE.
Examples
readRepeatdb(repeatfile = ~/test/chicken_raw.rdb, includeSimpleRepeats = TRUE, includeUnknownClass = FALSE)
readTSSdb Function for converting annotation file from DBTSS to specific data
frame
Description
This function allows you to converting TSS database file (tab file type) to data frame for analysis.
User can download TSS database file from DBTSS.
Usage
readTSSdb(inputfile)
Arguments
inputfile Full path of transcription start site database file(text file format) from DBTSS.
readTSSdb 13
Examples
readTSSdb(inputfile = ~/test/human_HEK293.tab)
Index
∗Topic BLASTn,
findHits,6
∗Topic CD-HIT-EST,
findHits,6
∗Topic CpG
readCpGdb,11
∗Topic DBTSS
readTSSdb,12
∗Topic GFF,
drawingIdeo,4
readGFF,11
∗Topic Genome
canine,2
chicken,2
human,7
monkey,9
mouse,9
∗Topic Ideogram
drawingIdeo,4
∗Topic NCBI
canine,2
chicken,2
drawingIdeo,4
human,7
monkey,9
mouse,9
readGFF,11
∗Topic Refseq,
canine,2
chicken,2
drawingIdeo,4
human,7
monkey,9
mouse,9
∗Topic Refseq
readGFF,11
∗Topic Repeats,
readRepeatdb,12
∗Topic TSS,
readTSSdb,12
∗Topic Transcription
readTSSdb,12
∗Topic UCSC
canine,2
chicken,2
human,7
monkey,9
mouse,9
readCpGdb,11
readRepeatdb,12
∗Topic browser
canine,2
chicken,2
human,7
monkey,9
mouse,9
readCpGdb,11
readRepeatdb,12
∗Topic database
readCpGdb,11
readGFF,11
readRepeatdb,12
∗Topic genome
readCpGdb,11
readRepeatdb,12
∗Topic islands,
readCpGdb,11
∗Topic megablast
findHits,6
∗Topic site,
readTSSdb,12
∗Topic sites,
readCpGdb,11
∗Topic start
readTSSdb,12
canine,2
chicken,2
chisq.test,10
14
