Example of a LowMACA object

Description

An object of class LowMACA of the alignment and mapping of the homeobox domain. It is the example used in the vignette.

Usage

data("lmObj")

Format

An object of class LowMACA

Source

Created by LowMACA package

Examples

#Load lmObj and show its structure
data(lmObj)
str(lmObj)

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)

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Type 'license()' or 'licence()' for distribution details.

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(LowMACA)
Checking if clustalo is in the PATH...
Checking perl installation...
Checking perl modules XML::Simple and LWP...
Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .).
BEGIN failed--compilation aborted.
Warning messages:
1: In .ClustalChecks(ClustalCommand = "clustalo") :
  Clustal Omega is not in the PATH:
You can either change clustalo command using lmParams function or use the web service. See ?setup
2: running command '/usr/bin/perl -MXML::Simple -e 1' had status 2 
3: In .PerlModuleChecks(stop = FALSE, perl = "perl") :
  XML::Simple module for perl is not installed. 
            If you don't want to install a local clustal omega and use the web service, XML::Simple is required

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/LowMACA/lmObj.Rd_%03d_medium.png", width=480, height=480)
> ### Name: lmObj
> ### Title: Example of a LowMACA object
> ### Aliases: lmObj
> ### Keywords: datasets
> 
> ### ** Examples
> 
> #Load lmObj and show its structure
> data(lmObj)
> str(lmObj)
Formal class 'LowMACA' [package "LowMACA"] with 4 slots
  ..@ arguments:List of 6
  .. ..$ genes      : NULL
  .. ..$ pfam       : chr "PF00046"
  .. ..$ input      :'data.frame':	28 obs. of  7 variables:
  .. .. ..$ Gene_Symbol   : Factor w/ 27 levels "ADNP","ALX1",..: 4 13 13 12 8 5 6 19 20 23 ...
  .. .. ..$ Pfam_ID       : Factor w/ 1 level "PF00046": 1 1 1 1 1 1 1 1 1 1 ...
  .. .. ..$ Entrez        : Factor w/ 27 levels "1046","1406",..: 25 26 26 27 15 1 2 7 8 11 ...
  .. .. ..$ Envelope_Start: chr [1:28] "79" "16" "102" "34" ...
  .. .. ..$ Envelope_End  : chr [1:28] "135" "70" "156" "90" ...
  .. .. ..$ UNIPROT       : Factor w/ 27 levels "ADNP_HUMAN","ALX1_HUMAN",..: 4 13 13 12 8 5 6 19 20 23 ...
  .. .. ..$ AMINO_SEQ     : chr [1:28] "HKERTSFTHQQYEELEALFSQTMFPDRNLQEKLALRLDLPESTVKVWFRNRRFKLKK" "RRCRTKFTEEQLKILINTFNQKPYPGYATKQKLALEINTEESRIQIWFQNRRARH" "RRCRTTYSASQLHTLIKAFMKNPYPGIDSREELAKEIGVPESRVQIWFQNRRSRL" "RRNRTTFTLQQLEALEAVFAQTHYPDVFTREELAMKINLTEARVQVWFQNRRAKWRK" ...
  .. ..$ mode       : chr "pfam"
  .. ..$ params     :List of 7
  .. .. ..$ mutation_type      : chr "missense"
  .. .. ..$ tumor_type         : chr [1:7] "skcm" "stad" "ucec" "luad" ...
  .. .. ..$ min_mutation_number: num 0
  .. .. ..$ density_bw         : num 0
  .. .. ..$ clustal_cmd        : chr "clustalo"
  .. .. ..$ use_hmm            : logi FALSE
  .. .. ..$ datum              : logi FALSE
  .. ..$ parallelize:List of 2
  .. .. ..$ getMutations : logi FALSE
  .. .. ..$ makeAlignment: logi TRUE
  ..@ alignment:List of 4
  .. ..$ ALIGNMENT:'data.frame':	1708 obs. of  8 variables:
  .. .. ..$ domainID      : Factor w/ 28 levels "ARGFX|PF00046|503582|79;135",..: 1 1 1 1 1 1 1 1 1 1 ...
  .. .. ..$ Gene_Symbol   : Factor w/ 27 levels "ADNP","ALX1",..: 4 4 4 4 4 4 4 4 4 4 ...
  .. .. ..$ Pfam          : Factor w/ 1 level "PF00046": 1 1 1 1 1 1 1 1 1 1 ...
  .. .. ..$ Entrez        : Factor w/ 27 levels "1046","127343",..: 21 21 21 21 21 21 21 21 21 21 ...
  .. .. ..$ Envelope_Start: num [1:1708] 79 79 79 79 79 79 79 79 79 79 ...
  .. .. ..$ Envelope_End  : num [1:1708] 135 135 135 135 135 135 135 135 135 135 ...
  .. .. ..$ Align         : int [1:1708] 1 2 3 4 5 6 7 8 9 10 ...
  .. .. ..$ Ref           : num [1:1708] 79 80 81 82 83 84 85 86 87 88 ...
  .. ..$ SCORE    :List of 2
  .. .. ..$ DIST_MAT     : num [1:28, 1:28] NA 36.4 34.5 50.9 26.3 ...
  .. .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. .. ..$ : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
  .. .. .. .. ..$ : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
  .. .. ..$ SUMMARY_SCORE:'data.frame':	28 obs. of  4 variables:
  .. .. .. ..$ MEAN_SIMILARITY  : num [1:28] 39.5 37.6 40.1 47.6 27.4 ...
  .. .. .. ..$ MEDIAN_SIMILARITY: num [1:28] 38.6 36.4 40 43.9 26.3 ...
  .. .. .. ..$ MAX_SIMILARITY   : num [1:28] 54.4 54.5 54.5 78.9 80.7 ...
  .. .. .. ..$ MIN_SIMILARITY   : num [1:28] 21.1 18.2 23.6 21.1 17.5 ...
  .. ..$ CLUSTAL  :Formal class 'AAMultipleAlignment' [package "Biostrings"] with 3 slots
  .. .. .. ..@ unmasked:Formal class 'AAStringSet' [package "Biostrings"] with 5 slots
  .. .. .. .. .. ..@ pool           :Formal class 'SharedRaw_Pool' [package "XVector"] with 2 slots
  .. .. .. .. .. .. .. ..@ xp_list                    :List of 1
  .. .. .. .. .. .. .. .. ..$ :<externalptr> 
  .. .. .. .. .. .. .. ..@ .link_to_cached_object_list:List of 1
  .. .. .. .. .. .. .. .. ..$ :<environment: 0xcf27540> 
  .. .. .. .. .. ..@ ranges         :Formal class 'GroupedIRanges' [package "XVector"] with 7 slots
  .. .. .. .. .. .. .. ..@ group          : int [1:28] 1 1 1 1 1 1 1 1 1 1 ...
  .. .. .. .. .. .. .. ..@ start          : int [1:28] 1 62 123 184 245 306 367 428 489 550 ...
  .. .. .. .. .. .. .. ..@ width          : int [1:28] 61 61 61 61 61 61 61 61 61 61 ...
  .. .. .. .. .. .. .. ..@ NAMES          : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
  .. .. .. .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. .. ..@ elementType    : chr "AAString"
  .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. ..@ metadata       : list()
  .. .. .. ..@ rowmask :Formal class 'NormalIRanges' [package "IRanges"] with 6 slots
  .. .. .. .. .. ..@ start          : int(0) 
  .. .. .. .. .. ..@ width          : int(0) 
  .. .. .. .. .. ..@ NAMES          : NULL
  .. .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. ..@ metadata       : list()
  .. .. .. ..@ colmask :Formal class 'NormalIRanges' [package "IRanges"] with 6 slots
  .. .. .. .. .. ..@ start          : int(0) 
  .. .. .. .. .. ..@ width          : int(0) 
  .. .. .. .. .. ..@ NAMES          : NULL
  .. .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. ..@ metadata       : list()
  .. ..$ df       :'data.frame':	61 obs. of  2 variables:
  .. .. ..$ consensus   : Factor w/ 18 levels "A","D","E","F",..: 13 13 1 13 15 1 4 15 14 3 ...
  .. .. ..$ conservation: num [1:61] 0.326 0.472 0.156 0.883 0.652 ...
  ..@ mutations:List of 3
  .. ..$ data   :'data.frame':	1389 obs. of  8 variables:
  .. .. ..$ Entrez             : int [1:1389] 3199 3213 91464 23316 127343 3232 23316 644168 139324 3199 ...
  .. .. ..$ Gene_Symbol        : chr [1:1389] "HOXA2" "HOXB3" "ISX" "CUX2" ...
  .. .. ..$ Amino_Acid_Letter  : chr [1:1389] "L" "S" "P" "R" ...
  .. .. ..$ Amino_Acid_Position: num [1:1389] 298 123 186 874 165 ...
  .. .. ..$ Amino_Acid_Change  : chr [1:1389] "L298M" "S123F" "P186A" "R874C" ...
  .. .. ..$ Mutation_Type      : chr [1:1389] "Missense_Mutation" "Missense_Mutation" "Missense_Mutation" "Missense_Mutation" ...
  .. .. ..$ Sample             : chr [1:1389] "SA236" "SA212" "SA229" "BR-M-166" ...
  .. .. ..$ Tumor_Type         : chr [1:1389] "brca" "brca" "brca" "brca" ...
  .. ..$ freq   :'data.frame':	7 obs. of  29 variables:
  .. .. ..$ StudyID                : Factor w/ 7 levels "brca","coadread",..: 1 2 3 4 5 6 7
  .. .. ..$ Total_Sequenced_Samples: int [1:7] 1262 296 513 178 559 438 248
  .. .. ..$ ADNP                   : int [1:7] 11 11 6 2 10 11 11
  .. .. ..$ ALX1                   : int [1:7] 2 4 10 6 3 7 8
  .. .. ..$ ALX4                   : int [1:7] 2 4 10 2 6 10 6
  .. .. ..$ ARGFX                  : int [1:7] 3 5 9 0 19 2 2
  .. .. ..$ CDX4                   : int [1:7] 2 0 11 3 24 7 9
  .. .. ..$ CRX                    : int [1:7] 3 4 9 3 13 9 4
  .. .. ..$ CUX1                   : int [1:7] 3 11 21 8 32 21 21
  .. .. ..$ CUX2                   : int [1:7] 7 9 19 3 59 21 7
  .. .. ..$ DBX2                   : int [1:7] 3 3 12 0 22 4 5
  .. .. ..$ DLX5                   : int [1:7] 3 3 12 4 8 7 1
  .. .. ..$ DMBX1                  : int [1:7] 2 3 5 2 23 3 7
  .. .. ..$ DRGX                   : int [1:7] 5 5 4 2 16 2 3
  .. .. ..$ DUXA                   : int [1:7] 2 2 8 6 12 3 5
  .. .. ..$ ESX1                   : int [1:7] 2 9 7 2 13 7 3
  .. .. ..$ EVX2                   : int [1:7] 0 2 6 2 14 12 7
  .. .. ..$ HDX                    : int [1:7] 11 12 18 6 10 8 19
  .. .. ..$ HLX                    : int [1:7] 3 10 7 4 7 6 8
  .. .. ..$ HOXA1                  : int [1:7] 3 4 11 3 14 7 9
  .. .. ..$ HOXA2                  : int [1:7] 5 2 14 1 7 2 5
  .. .. ..$ HOXA3                  : int [1:7] 1 5 11 4 18 8 3
  .. .. ..$ HOXA5                  : int [1:7] 3 4 19 0 9 3 1
  .. .. ..$ HOXB1                  : int [1:7] 0 0 14 4 14 6 2
  .. .. ..$ HOXB3                  : int [1:7] 4 2 14 3 10 4 2
  .. .. ..$ HOXD3                  : int [1:7] 2 3 8 3 9 7 6
  .. .. ..$ ISL1                   : int [1:7] 4 11 9 2 10 4 4
  .. .. ..$ ISX                    : int [1:7] 3 2 5 5 27 2 5
  .. .. ..$ LHX8                   : int [1:7] 2 5 15 6 12 9 7
  .. ..$ aligned: num [1:28, 1:61] 0 0 1 0 0 1 0 0 0 1 ...
  .. .. ..- attr(*, "dimnames")=List of 2
  .. .. .. ..$ : chr [1:28] "ARGFX|PF00046|503582|79;135" "DUXA|PF00046|503835|16;70" "DUXA|PF00046|503835|102;156" "DRGX|PF00046|644168|34;90" ...
  .. .. .. ..$ : NULL
  ..@ entropy  : list()
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>