AIRs Ref Manual

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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 
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 genomic 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

R topics documented:
canine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
chicken . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
1

2
2
3

2

chicken
drawingIdeo . .
extractFeatures
FASTAinfo . .
findHits . . . .
human . . . . .
makeHitTable .
monkey . . . .
mouse . . . . .
random . . . .
readCpGdb . .
readGFF . . . .
readRepeatdb .
readTSSdb . . .

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Index

canine

14

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)

4
5
6
6
7
8
9
9
10
11
11
12
12

distribution

3

Format
An object of class data.frame with 8064 rows and 2 columns.
Examples
data(chicken)

Functions for distribution analysis

distribution

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
annoHitTable
annotTableType
isHuman
featureTable
interval
outputpath

Data frame of BLAST result (from makeHitTable_output$rawHits).
Data frame of annotated hits (from makeHitTable_output$annoHits).
Choose one of genetical features such as gene, cpg, repeat, tss.
If target genome is human, enter TRUE. Default is FALSE.
Data frame of annotation databases.
Interval of distribution graph. User can choose 2kb or 5kb. Default is 2kb.
Full path of output file located (Except for file name). Default is working directory.

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)

4

drawingIdeo

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 directory.

See Also
findHits
makeHitTable
extractFeatures

Examples
drawingIdeo(anno$region, anno$genes, hitset$rawHits, blastdb = ncbi, chicken, outputpath = ~/test)

extractFeatures

5

Function for making various type data table from NCBI Refseq annotation file.

extractFeatures

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)

6

findHits

Function for profiling FASTA file

FASTAinfo

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 directory.

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)

8

makeHitTable

Function for making hit table about integrated regions into genomic
factors.

makeHitTable

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 running 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

monkey

9

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

Function for random analysis

random

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 directory.

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

readCpGdb

11

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
select

Full path of CpG site database file(text file format) from UCSC genome browser.
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
nrows

Full path of target’s annotation file (GFF format).
Do not modify negative value of this.

See Also
extractFeatures
Examples
readGFF(gffFile = ~/test/chicken.gff)

12

readTSSdb

Function for converting annotation file from UCSC to specific data
frame

readRepeatdb

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)

Function for converting annotation file from DBTSS to specific data
frame

readTSSdb

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
Examples
readTSSdb(inputfile = ~/test/human_HEK293.tab)

13

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

INDEX
distribution, 3, 7, 10
drawingIdeo, 4, 5, 7
extractFeatures, 4, 5, 8, 11
FASTAinfo, 6
findHits, 3, 4, 6, 8, 10
GenomicRanges, 8
human, 7
makeHitTable, 3, 4, 7, 8, 10
monkey, 9
mouse, 9
random, 7, 10
readCpGdb, 11
readGFF, 5, 11
readRepeatdb, 12
readTSSdb, 12

15
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