pfamDomains: pfam domain annotation and summarization.
In maftools: Summarize, Analyze and Visualize MAF Files
Description
Usage
Arguments
Value
Examples
View source: R/domainSummary.R
Description
Summarizes amino acid positions and annotates them with pfam domain information.
Usage
1
2
3
4
5
6
7
8
9
10
11
12
Arguments
maf
an MAF object generated by read.maf
AACol
manually specify column name for amino acid changes. Default looks for field 'AAChange'
summarizeBy
Summarize domains by amino acid position or conversions. Can be "AAPos" or "AAChange"
top
How many top mutated domains to label in the scatter plot. Defaults to 5.
domainsToLabel
Default NULL. Exclusive with top argument.
baseName
If given writes the results to output file. Default NULL.
varClass
which variants to consider for summarization. Can be nonSyn, Syn or all. Default nonSyn.
width
width of the file to be saved.
height
height of the file to be saved.
labelSize
font size for labels. Default 1.
Value
returns a list two tables summarized by amino acid positions and domains respectively. Also plots top 5 most mutated domains as scatter plot.
Examples
1
2
3
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
pfamDomains(maf = laml, AACol = 'Protein_Change')
Example output
-Reading
-Validating
-Silent variants: 475
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.398s elapsed (0.373s cpu)
Warning in pfamDomains(maf = laml, AACol = "Protein_Change") :
Removed 50 mutations for which AA position was not available
$proteinSummary
HGNC AAPos Variant_Classification N total fraction DomainLabel
1: DNMT3A 882 Missense_Mutation 27 54 0.5000000 AdoMet_MTases
2: IDH1 132 Missense_Mutation 18 18 1.0000000 PTZ00435
3: IDH2 140 Missense_Mutation 17 20 0.8500000 PTZ00435
4: FLT3 835 Missense_Mutation 14 52 0.2692308 PKc_like
5: FLT3 599 In_Frame_Ins 10 52 0.1923077 PKc_like
---
1512: ZNF646 875 Missense_Mutation 1 1 1.0000000 <NA>
1513: ZNF687 554 Missense_Mutation 1 2 0.5000000 <NA>
1514: ZNF687 363 Missense_Mutation 1 2 0.5000000 <NA>
1515: ZNF75D 5 Missense_Mutation 1 1 1.0000000 <NA>
1516: ZNF827 427 Frame_Shift_Del 1 1 1.0000000 <NA>
pfam
1: AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)
2: Provisional
3: Provisional
4: cl09925
5: cl09925
---
1512: <NA>
1513: <NA>
1514: <NA>
1515: <NA>
1516: <NA>
Description
1: S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I
2: isocitrate dehydrogenase
3: isocitrate dehydrogenase
4: Protein Kinases, catalytic domain
5: Protein Kinases, catalytic domain
---
1512: <NA>
1513: <NA>
1514: <NA>
1515: <NA>
1516: <NA>
$domainSummary
DomainLabel nMuts nGenes
1: PKc_like 55 5
2: PTZ00435 38 2
3: AdoMet_MTases 33 1
4: 7tm_1 24 24
5: COG5048 17 17
---
499: ribokinase 1 1
500: rim_protein 1 1
501: sigpep_I_bact 1 1
502: trp 1 1
503: zf-BED 1 1
pfam
1: cl09925
2: Provisional
3: AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)
4: pfam00001
5: <NA>
---
499: cd01174
500: TIGR01257
501: TIGR02227
502: TIGR00870
503: pfam02892
Description
1: Protein Kinases, catalytic domain
2: isocitrate dehydrogenase
3: S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I
4: 7 transmembrane receptor (rhodopsin family)
5: FOG: Zn-finger [General function prediction only]
---
499: Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...
500: retinal-specific rim ABC transporter
501: signal peptidase I, bacterial type
502: transient-receptor-potential calcium channel protein
503: BED zinc finger
maftools documentation built on Feb. 6, 2021, 2 a.m.
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Description Usage Arguments Value Examples
View source: R/domainSummary.R
Description
Summarizes amino acid positions and annotates them with pfam domain information.
Usage
1 2 3 4 5 6 7 8 9 10 11 12 |
Arguments
maf |
an |
AACol |
manually specify column name for amino acid changes. Default looks for field 'AAChange' |
summarizeBy |
Summarize domains by amino acid position or conversions. Can be "AAPos" or "AAChange" |
top |
How many top mutated domains to label in the scatter plot. Defaults to 5. |
domainsToLabel |
Default NULL. Exclusive with top argument. |
baseName |
If given writes the results to output file. Default NULL. |
varClass |
which variants to consider for summarization. Can be nonSyn, Syn or all. Default nonSyn. |
width |
width of the file to be saved. |
height |
height of the file to be saved. |
labelSize |
font size for labels. Default 1. |
Value
returns a list two tables summarized by amino acid positions and domains respectively. Also plots top 5 most mutated domains as scatter plot.
Examples
1 2 3 | laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
pfamDomains(maf = laml, AACol = 'Protein_Change')
|
Example output
-Reading
-Validating
-Silent variants: 475
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.398s elapsed (0.373s cpu)
Warning in pfamDomains(maf = laml, AACol = "Protein_Change") :
Removed 50 mutations for which AA position was not available
$proteinSummary
HGNC AAPos Variant_Classification N total fraction DomainLabel
1: DNMT3A 882 Missense_Mutation 27 54 0.5000000 AdoMet_MTases
2: IDH1 132 Missense_Mutation 18 18 1.0000000 PTZ00435
3: IDH2 140 Missense_Mutation 17 20 0.8500000 PTZ00435
4: FLT3 835 Missense_Mutation 14 52 0.2692308 PKc_like
5: FLT3 599 In_Frame_Ins 10 52 0.1923077 PKc_like
---
1512: ZNF646 875 Missense_Mutation 1 1 1.0000000 <NA>
1513: ZNF687 554 Missense_Mutation 1 2 0.5000000 <NA>
1514: ZNF687 363 Missense_Mutation 1 2 0.5000000 <NA>
1515: ZNF75D 5 Missense_Mutation 1 1 1.0000000 <NA>
1516: ZNF827 427 Frame_Shift_Del 1 1 1.0000000 <NA>
pfam
1: AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)
2: Provisional
3: Provisional
4: cl09925
5: cl09925
---
1512: <NA>
1513: <NA>
1514: <NA>
1515: <NA>
1516: <NA>
Description
1: S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I
2: isocitrate dehydrogenase
3: isocitrate dehydrogenase
4: Protein Kinases, catalytic domain
5: Protein Kinases, catalytic domain
---
1512: <NA>
1513: <NA>
1514: <NA>
1515: <NA>
1516: <NA>
$domainSummary
DomainLabel nMuts nGenes
1: PKc_like 55 5
2: PTZ00435 38 2
3: AdoMet_MTases 33 1
4: 7tm_1 24 24
5: COG5048 17 17
---
499: ribokinase 1 1
500: rim_protein 1 1
501: sigpep_I_bact 1 1
502: trp 1 1
503: zf-BED 1 1
pfam
1: cl09925
2: Provisional
3: AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy)
4: pfam00001
5: <NA>
---
499: cd01174
500: TIGR01257
501: TIGR02227
502: TIGR00870
503: pfam02892
Description
1: Protein Kinases, catalytic domain
2: isocitrate dehydrogenase
3: S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I
4: 7 transmembrane receptor (rhodopsin family)
5: FOG: Zn-finger [General function prediction only]
---
499: Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides...
500: retinal-specific rim ABC transporter
501: signal peptidase I, bacterial type
502: transient-receptor-potential calcium channel protein
503: BED zinc finger
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