Summary of example data sets.

Description

Explaining example data of PepPrep package.

Details

‘ExampleData.RData’ contains a data.frame called testtbl (annotated single nucleotide variant (SNV)).
Columns in testtbl:
Chr: Chromosom number
Start: Startposition
End: Endposition
Ref: Nucleotide in referencegenome
Obs: Observed Nucleotide
AAChange: Information from ANNOVAR it should look like NM_ID:c.Ref_Pos_Obs:p.RefAminoacid_Pos_MutAminoacid
Gene: Gene name

‘ExampleHomo_sapiens.GRCh37.70.pep.all.fa’
Contains the Ensembl protein ENSP00000361883 in FASTA format

‘ExampleHumanProt.fasta’
Two human protein sequneces from UniProt.

‘ExampleMouseProt.fasta’
Two mouse protein sequences from UniProt.

Examples

testtbl <- system.file("extdata", "ExampleData.RData", package="PepPrep")
load(testtbl)
testtbl
attributes(testtbl)
lapply(testtbl,class)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(PepPrep)
Loading required package: biomaRt
Loading required package: stringr
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/PepPrep/ExampleDataSets.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ExampleDataSets
> ### Title: Summary of example data sets.
> ### Aliases: ExampleDataSets
> ### Keywords: datasets
> 
> ### ** Examples
> 
> testtbl <- system.file("extdata", "ExampleData.RData", package="PepPrep")
> load(testtbl)
> testtbl
     Chr     Start       End Ref Obs
231    1  40533266  40533266   T   G
232    1  40533287  40533287   T   G
233    1  40533315  40533315   T   G
234    1  40533320  40533320   T   G
235    1  40533326  40533326   T   G
236    1  40533347  40533347   T   G
820    1 223717484 223717484   G   A
821    1 223718651 223718651   G   A
822    1 223900408 223900408   C   G
1021   2  30957326  30957326   A   G
1022   2  30975961  30975961   G   T
1466   2 241538074 241538074   A   G
2564   5  35910529  35910529   C   T
3319   6  44151490  44151490   G   A
4144   7 158464295 158464295   G   A
5858  12   6619284   6619284   C   G
6025  12  30881809  30881809   T   C
6196  12  75715330  75715330   C   A
6854  15  42681199  42681199   G   A
8517  19  39228228  39228228   G   A
8518  19  39232421  39232421   C   T
9425  22  50960682  50960682   C   T
                                                                     Gene
231                                                                  CAP1
232                                                                  CAP1
233                                                                  CAP1
234                                                                  CAP1
235                                                                  CAP1
236                                                                  CAP1
820                                                                 CAPN8
821                                                                 CAPN8
822                                                                 CAPN2
1021                                                               CAPN13
1022                                                               CAPN13
1466                                                               CAPN10
2564                                                                CAPSL
3319                                                               CAPN11
4144                                                               NCAPG2
5858                                                               NCAPD2
6025                                                              CAPRIN2
6196                                                                CAPS2
6854                                                                CAPN3
8517                                                               CAPN12
8518                                                               CAPN12
9425 NCAPH2(NM_001185011:exon14:c.1233+2C>T;NM_152299:exon14:c.1233+2C>T)
                          AAChange
231   NM_001105530:c.T685G:p.C229G
232   NM_001105530:c.T706G:p.C236G
233   NM_001105530:c.T734G:p.I245S
234   NM_001105530:c.T739G:p.C247G
235   NM_001105530:c.T745G:p.Y249D
236   NM_001105530:c.T766G:p.S256A
820                        UNKNOWN
821                        UNKNOWN
822        NM_001748:c.C66G:p.D22E
1021    NM_144575:c.T1787C:p.I596T
1022    NM_144575:c.C1045A:p.Q349K
1466    NM_023085:c.A1531G:p.I511V
2564   NM_001042625:c.G254A:p.R85Q
3319    NM_007058:c.G2183A:p.S728N
4144    NM_017760:c.C1390T:p.L464F
5858      NM_014865:c.C247G:p.Q83E
6025 NM_001002259:c.A1555G:p.M519V
6196     NM_032606:c.G375T:p.L125F
6854     NM_000070:c.G706A:p.A236T
8517    NM_144691:c.C1016T:p.S339L
8518     NM_144691:c.G556A:p.A186T
9425                              
> attributes(testtbl)
$names
[1] "Chr"      "Start"    "End"      "Ref"      "Obs"      "Gene"     "AAChange"

$row.names
 [1]  231  232  233  234  235  236  820  821  822 1021 1022 1466 2564 3319 4144
[16] 5858 6025 6196 6854 8517 8518 9425

$class
[1] "data.frame"

> lapply(testtbl,class)
$Chr
[1] "character"

$Start
[1] "integer"

$End
[1] "integer"

$Ref
[1] "character"

$Obs
[1] "character"

$Gene
[1] "character"

$AAChange
[1] "character"

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>