README.md
In kingyang728/genomicCoordinateConverter: Coordinate Converter
genomicCoordinateConverter
The goal of genomicCoordinateConverter is to provide functionalities
supporting convert coordinate to amino acid information.The package
contains 6 main converter functionalities: * genomic location
(default genome: HG38), nucleotide exchange -> HUGO Symbol, transcript
ID, position in primary transcript, exchanged amino acid *
genomic location (default genome: HG38), nucleotide exchange -> HUGO
Symbol, for all transcripts :transcript ID, position exchanged amino
acid * genomic location (default genome: HG38) -> HUGO Symbol,
list of all transcript ID * genomic location (default genome:
HG38), nucleotide exchange -> HUGO symbol, exon number *
transcript ID, position , target genome -> genomic location, triplet
and number in triplet * Genomeversion, genomic location, taget
genomeversion -> genomic location
Installation
You can install the development version from
GitHub with:
# install.packages("devtools")
devtools::install_github("kingyang728/genomicCoordinateConverter")
Example
This is a basic example which shows you how to convert genomic
coordinate to target dataframe:
library(genomicCoordinateConverter)
#>
#>
## basic example code
#genomic location, nucleotide exchange -> HUGO Symbol, transcript ID, position in primary transcript, exchanged amino acid
Coordinate_Covnerter1("chrX",48823056,48823056,"G","C")
#> Import genomic features from the file as a GRanges object ...
#> OK
#> Prepare the 'metadata' data frame ... OK
#> Make the TxDb object ...
#> Warning in .extract_exons_from_GRanges(exon_IDX, gr, mcols0, tx_IDX, feature = "exon", : 1922 exons couldn't be linked to a transcript so were dropped (showing
#> only the first 6):
#> seqid start end strand ID Name Parent
#> 1 1 2566410 2566605 + <NA> ENSE00001889931 transcript:ENST00000456687
#> 2 1 2567866 2568054 + <NA> ENSE00001659318 transcript:ENST00000456687
#> 3 1 2568977 2569888 + <NA> ENSE00001624410 transcript:ENST00000456687
#> 4 1 3205988 3208664 + <NA> ENSE00003757578 transcript:ENST00000624175
#> 5 1 9826289 9828271 - <NA> ENSE00003807109 transcript:ENST00000639753
#> 6 1 9827610 9828258 - <NA> ENSE00003759368 transcript:ENST00000623863
#> Parent_type
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> Warning in .extract_exons_from_GRanges(cds_IDX, gr, mcols0, tx_IDX, feature = "cds", : 752 CDS couldn't be linked to a transcript so were dropped (showing
#> only the first 6):
#> seqid start end strand ID Name
#> 1 14 21621904 21621946 + CDS:ENSP00000446309 ENSP00000446309
#> 2 14 21622285 21622567 + CDS:ENSP00000446309 ENSP00000446309
#> 3 14 21642973 21643015 + CDS:ENSP00000439668 ENSP00000439668
#> 4 14 21643304 21643578 + CDS:ENSP00000439668 ENSP00000439668
#> 5 14 21712331 21712394 + CDS:ENSP00000438195 ENSP00000438195
#> 6 14 21712570 21712843 + CDS:ENSP00000438195 ENSP00000438195
#> Parent Parent_type
#> 1 transcript:ENST00000542354 <NA>
#> 2 transcript:ENST00000542354 <NA>
#> 3 transcript:ENST00000390423 <NA>
#> 4 transcript:ENST00000390423 <NA>
#> 5 transcript:ENST00000390424 <NA>
#> 6 transcript:ENST00000390424 <NA>
#> OK
#> Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 25 out-of-bound ranges located on sequences
#> 219562, 219565, 219570, 219571, and 219573. Note that ranges located on
#> a sequence whose length is unknown (NA) or on a circular sequence are
#> not considered out-of-bound (use seqlengths() and isCircular() to get
#> the lengths and circularity flags of the underlying sequences). You can
#> use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for
#> more information.
#> [1] "ENST00000376619" "ENST00000334136" "ENST00000643374" "ENST00000644068"
#> [5] "ENST00000643934"
#> seqnames start end Hugo_Symbol transcript_id TXstart TXend
#> 1 chrX 48823056 48823056 HDAC6 ENST00000334136 48802067 48824976
#> 2 chrX 48823056 48823056 HDAC6 ENST00000376619 48802034 48824976
#> 3 chrX 48823056 48823056 HDAC6 ENST00000643374 48802159 48824956
#> 4 chrX 48823056 48823056 HDAC6 ENST00000643934 48802187 48824958
#> 5 chrX 48823056 48823056 HDAC6 ENST00000644068 48802168 48824976
#> CDS_position RefAminoAcid VarAminoAcid
#> 1 2657 S S
#> 2 2657 S S
#> 3 2657 S S
#> 4 2492 S S
#> 5 2657 S S
#genomic location, nucleotide exchange -> HUGO Symbol, for all transcripts :transcript ID, position exchanged amino acid
Coordinate_Covnerter2("chrX",48823056,48823056,"G","C")
#> Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 25 out-of-bound ranges located on sequences
#> 219562, 219565, 219570, 219571, and 219573. Note that ranges located on
#> a sequence whose length is unknown (NA) or on a circular sequence are
#> not considered out-of-bound (use seqlengths() and isCircular() to get
#> the lengths and circularity flags of the underlying sequences). You can
#> use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for
#> more information.
#> [1] "ENST00000376619" "ENST00000334136" "ENST00000643374" "ENST00000644068"
#> [5] "ENST00000643934"
#> seqnames start end Hugo_Symbol PROTEINLOC transcript_id
#> 1 chrX 48823056 48823056 HDAC6 886 ENST00000376619
#> 2 chrX 48823056 48823056 HDAC6 886 ENST00000334136
#> 3 chrX 48823056 48823056 HDAC6 886 ENST00000643374
#> 4 chrX 48823056 48823056 HDAC6 886 ENST00000644068
#> 5 chrX 48823056 48823056 HDAC6 831 ENST00000643934
#genomic location -> HUGO Symbol, list of all transcript ID
Coordinate_Covnerter3("chrX",48823056,48823056)
#> seqnames start end transcript_id Hugo_Symbol
#> 2851349 chrX 48802034 48824976 ENST00000376619 HDAC6
#> 2851410 chrX 48802055 48824982 ENST00000477528 HDAC6
#> 2851454 chrX 48802067 48824976 ENST00000334136 HDAC6
#> 2851555 chrX 48802133 48824860 ENST00000643659 HDAC6
#> 2851585 chrX 48802159 48824956 ENST00000643374 HDAC6
#> 2851646 chrX 48802168 48824976 ENST00000644068 HDAC6
#> 2851722 chrX 48802187 48824958 ENST00000643934 HDAC6
#> 2851831 chrX 48802888 48824967 ENST00000647398 HDAC6
#> 2851907 chrX 48813353 48824976 ENST00000486227 HDAC6
#> 2851953 chrX 48816470 48824947 ENST00000645643 HDAC6
#> 2851998 chrX 48818071 48823109 ENST00000480525 HDAC6
#> 2852006 chrX 48818313 48823579 ENST00000498808 HDAC6
#> 2852012 chrX 48819447 48824976 ENST00000488543 HDAC6
#genomic location (default genome: HG38), nucleotide exchange -> HUGO symbol, exon number
Coordinate_Covnerter4("chrX",48823056,48823056)
#> seqnames start end exon_id rank
#> 2851399 chrX 48822912 48823588 ENSE00003465573 25
#> 2851434 chrX 48822912 48823588 ENSE00003634146 24
#> 2851504 chrX 48822912 48823588 ENSE00003465573 25
#> 2851580 chrX 48822912 48823588 ENSE00003634146 25
#> 2851635 chrX 48822912 48823588 ENSE00003465573 25
#> 2851696 chrX 48822912 48823588 ENSE00003465573 25
#> 2851770 chrX 48822912 48823588 ENSE00003465573 24
#> 2851920 chrX 48822912 48823588 ENSE00003634146 13
#> 2851965 chrX 48822912 48823588 ENSE00003634146 6
#> 2852004 chrX 48822912 48823109 ENSE00001839278 3
#> 2852015 chrX 48822912 48823588 ENSE00003634146 3
#transcript ID, position , target genome -> genomic location, triplet and number in triplet
##transcript id passed in should be ensembl transcript id like "ENST00000334136"
Coordinate_Covnerter5_2("ENST00000334136",2657)
#> Warning: `select_()` is deprecated as of dplyr 0.7.0.
#> Please use `select()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_warnings()` to see where this warning was generated.
#> Warning: `filter_()` is deprecated as of dplyr 0.7.0.
#> Please use `filter()` instead.
#> See vignette('programming') for more help
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_warnings()` to see where this warning was generated.
#> Cache found
#> seqnames start end condon condonNumber
#> 1 chrX 48823056 48823056 TCA 2
#Genomeversion, genomic location, taget genomeversion -> genomic location
Coordinate_Covnerter6("chrX",45060024,45060024,"hg16","hg18")
#> seqnames start end width strand
#> 1 chrX 45898986 45898986 1 *
kingyang728/genomicCoordinateConverter documentation built on June 29, 2020, 4:05 a.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
genomicCoordinateConverter
The goal of genomicCoordinateConverter is to provide functionalities supporting convert coordinate to amino acid information.The package contains 6 main converter functionalities: * genomic location (default genome: HG38), nucleotide exchange -> HUGO Symbol, transcript ID, position in primary transcript, exchanged amino acid * genomic location (default genome: HG38), nucleotide exchange -> HUGO Symbol, for all transcripts :transcript ID, position exchanged amino acid * genomic location (default genome: HG38) -> HUGO Symbol, list of all transcript ID * genomic location (default genome: HG38), nucleotide exchange -> HUGO symbol, exon number * transcript ID, position , target genome -> genomic location, triplet and number in triplet * Genomeversion, genomic location, taget genomeversion -> genomic location
Installation
You can install the development version from GitHub with:
# install.packages("devtools")
devtools::install_github("kingyang728/genomicCoordinateConverter")
Example
This is a basic example which shows you how to convert genomic coordinate to target dataframe:
library(genomicCoordinateConverter)
#>
#>
## basic example code
#genomic location, nucleotide exchange -> HUGO Symbol, transcript ID, position in primary transcript, exchanged amino acid
Coordinate_Covnerter1("chrX",48823056,48823056,"G","C")
#> Import genomic features from the file as a GRanges object ...
#> OK
#> Prepare the 'metadata' data frame ... OK
#> Make the TxDb object ...
#> Warning in .extract_exons_from_GRanges(exon_IDX, gr, mcols0, tx_IDX, feature = "exon", : 1922 exons couldn't be linked to a transcript so were dropped (showing
#> only the first 6):
#> seqid start end strand ID Name Parent
#> 1 1 2566410 2566605 + <NA> ENSE00001889931 transcript:ENST00000456687
#> 2 1 2567866 2568054 + <NA> ENSE00001659318 transcript:ENST00000456687
#> 3 1 2568977 2569888 + <NA> ENSE00001624410 transcript:ENST00000456687
#> 4 1 3205988 3208664 + <NA> ENSE00003757578 transcript:ENST00000624175
#> 5 1 9826289 9828271 - <NA> ENSE00003807109 transcript:ENST00000639753
#> 6 1 9827610 9828258 - <NA> ENSE00003759368 transcript:ENST00000623863
#> Parent_type
#> 1 <NA>
#> 2 <NA>
#> 3 <NA>
#> 4 <NA>
#> 5 <NA>
#> 6 <NA>
#> Warning in .extract_exons_from_GRanges(cds_IDX, gr, mcols0, tx_IDX, feature = "cds", : 752 CDS couldn't be linked to a transcript so were dropped (showing
#> only the first 6):
#> seqid start end strand ID Name
#> 1 14 21621904 21621946 + CDS:ENSP00000446309 ENSP00000446309
#> 2 14 21622285 21622567 + CDS:ENSP00000446309 ENSP00000446309
#> 3 14 21642973 21643015 + CDS:ENSP00000439668 ENSP00000439668
#> 4 14 21643304 21643578 + CDS:ENSP00000439668 ENSP00000439668
#> 5 14 21712331 21712394 + CDS:ENSP00000438195 ENSP00000438195
#> 6 14 21712570 21712843 + CDS:ENSP00000438195 ENSP00000438195
#> Parent Parent_type
#> 1 transcript:ENST00000542354 <NA>
#> 2 transcript:ENST00000542354 <NA>
#> 3 transcript:ENST00000390423 <NA>
#> 4 transcript:ENST00000390423 <NA>
#> 5 transcript:ENST00000390424 <NA>
#> 6 transcript:ENST00000390424 <NA>
#> OK
#> Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 25 out-of-bound ranges located on sequences
#> 219562, 219565, 219570, 219571, and 219573. Note that ranges located on
#> a sequence whose length is unknown (NA) or on a circular sequence are
#> not considered out-of-bound (use seqlengths() and isCircular() to get
#> the lengths and circularity flags of the underlying sequences). You can
#> use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for
#> more information.
#> [1] "ENST00000376619" "ENST00000334136" "ENST00000643374" "ENST00000644068"
#> [5] "ENST00000643934"
#> seqnames start end Hugo_Symbol transcript_id TXstart TXend
#> 1 chrX 48823056 48823056 HDAC6 ENST00000334136 48802067 48824976
#> 2 chrX 48823056 48823056 HDAC6 ENST00000376619 48802034 48824976
#> 3 chrX 48823056 48823056 HDAC6 ENST00000643374 48802159 48824956
#> 4 chrX 48823056 48823056 HDAC6 ENST00000643934 48802187 48824958
#> 5 chrX 48823056 48823056 HDAC6 ENST00000644068 48802168 48824976
#> CDS_position RefAminoAcid VarAminoAcid
#> 1 2657 S S
#> 2 2657 S S
#> 3 2657 S S
#> 4 2492 S S
#> 5 2657 S S
#genomic location, nucleotide exchange -> HUGO Symbol, for all transcripts :transcript ID, position exchanged amino acid
Coordinate_Covnerter2("chrX",48823056,48823056,"G","C")
#> Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 25 out-of-bound ranges located on sequences
#> 219562, 219565, 219570, 219571, and 219573. Note that ranges located on
#> a sequence whose length is unknown (NA) or on a circular sequence are
#> not considered out-of-bound (use seqlengths() and isCircular() to get
#> the lengths and circularity flags of the underlying sequences). You can
#> use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for
#> more information.
#> [1] "ENST00000376619" "ENST00000334136" "ENST00000643374" "ENST00000644068"
#> [5] "ENST00000643934"
#> seqnames start end Hugo_Symbol PROTEINLOC transcript_id
#> 1 chrX 48823056 48823056 HDAC6 886 ENST00000376619
#> 2 chrX 48823056 48823056 HDAC6 886 ENST00000334136
#> 3 chrX 48823056 48823056 HDAC6 886 ENST00000643374
#> 4 chrX 48823056 48823056 HDAC6 886 ENST00000644068
#> 5 chrX 48823056 48823056 HDAC6 831 ENST00000643934
#genomic location -> HUGO Symbol, list of all transcript ID
Coordinate_Covnerter3("chrX",48823056,48823056)
#> seqnames start end transcript_id Hugo_Symbol
#> 2851349 chrX 48802034 48824976 ENST00000376619 HDAC6
#> 2851410 chrX 48802055 48824982 ENST00000477528 HDAC6
#> 2851454 chrX 48802067 48824976 ENST00000334136 HDAC6
#> 2851555 chrX 48802133 48824860 ENST00000643659 HDAC6
#> 2851585 chrX 48802159 48824956 ENST00000643374 HDAC6
#> 2851646 chrX 48802168 48824976 ENST00000644068 HDAC6
#> 2851722 chrX 48802187 48824958 ENST00000643934 HDAC6
#> 2851831 chrX 48802888 48824967 ENST00000647398 HDAC6
#> 2851907 chrX 48813353 48824976 ENST00000486227 HDAC6
#> 2851953 chrX 48816470 48824947 ENST00000645643 HDAC6
#> 2851998 chrX 48818071 48823109 ENST00000480525 HDAC6
#> 2852006 chrX 48818313 48823579 ENST00000498808 HDAC6
#> 2852012 chrX 48819447 48824976 ENST00000488543 HDAC6
#genomic location (default genome: HG38), nucleotide exchange -> HUGO symbol, exon number
Coordinate_Covnerter4("chrX",48823056,48823056)
#> seqnames start end exon_id rank
#> 2851399 chrX 48822912 48823588 ENSE00003465573 25
#> 2851434 chrX 48822912 48823588 ENSE00003634146 24
#> 2851504 chrX 48822912 48823588 ENSE00003465573 25
#> 2851580 chrX 48822912 48823588 ENSE00003634146 25
#> 2851635 chrX 48822912 48823588 ENSE00003465573 25
#> 2851696 chrX 48822912 48823588 ENSE00003465573 25
#> 2851770 chrX 48822912 48823588 ENSE00003465573 24
#> 2851920 chrX 48822912 48823588 ENSE00003634146 13
#> 2851965 chrX 48822912 48823588 ENSE00003634146 6
#> 2852004 chrX 48822912 48823109 ENSE00001839278 3
#> 2852015 chrX 48822912 48823588 ENSE00003634146 3
#transcript ID, position , target genome -> genomic location, triplet and number in triplet
##transcript id passed in should be ensembl transcript id like "ENST00000334136"
Coordinate_Covnerter5_2("ENST00000334136",2657)
#> Warning: `select_()` is deprecated as of dplyr 0.7.0.
#> Please use `select()` instead.
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_warnings()` to see where this warning was generated.
#> Warning: `filter_()` is deprecated as of dplyr 0.7.0.
#> Please use `filter()` instead.
#> See vignette('programming') for more help
#> This warning is displayed once every 8 hours.
#> Call `lifecycle::last_warnings()` to see where this warning was generated.
#> Cache found
#> seqnames start end condon condonNumber
#> 1 chrX 48823056 48823056 TCA 2
#Genomeversion, genomic location, taget genomeversion -> genomic location
Coordinate_Covnerter6("chrX",45060024,45060024,"hg16","hg18")
#> seqnames start end width strand
#> 1 chrX 45898986 45898986 1 *
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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