Mercurial > repos > kpbioteam > ewastools

comparison minfi_dmr.xml @ 63:2ee6ac5227f1 draft

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author kpbioteam
date Thu, 04 Apr 2019 11:20:23 -0400
parents 491cf4ada3a3
children 1334312dc198
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62:81a9b843e05c 63:2ee6ac5227f1
46 maxGap = maxGap, 46 maxGap = maxGap,
47 cutoff = cutoff, 47 cutoff = cutoff,
48 nullMethod = nullMethod, 48 nullMethod = nullMethod,
49 B = B) 49 B = B)
50 50
51 dmrGR <- with(dmrs\$table,GRanges(chr,IRanges(start,end),area=area,value=value)) 51 dmrGR <- dmrs\$table[,c(1,2,3)]
52 colnames(dmrGR) <- c("chr","start","end")
52 53
53 dmrGR <- as.data.frame(dmrGR) 54 write.table(dmrGR, file= '$dmr', quote = FALSE,col.names = TRUE, row.names = FALSE, sep = "\t")
54
55 colnames(dmrGR) <- c("seqnames","start","end","width","strand","area","value")
56
57 dmrGR\$strand <- NULL
58
59 dmrGR\$area <- NULL
60
61 write.table(dmrGR, file= '$dmr', quote = FALSE,col.names = FALSE, row.names = FALSE, sep = "\t")
62 ]]> 55 ]]>
63 </configfile> 56 </configfile>
64 </configfiles> 57 </configfiles>
65 <inputs> 58 <inputs>
66 <param type="data" name="grset" format="rdata" label="Genomic Ratio Set" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic 59 <param type="data" name="grset" format="rdata" label="Genomic Ratio Set" help="This class holds preprocessed data for Illumina methylation microarrays, mapped to a genomic
97 90
98 This tool is a version of the bump hunting algorithm (Andrew E Jaffe et al. 2012) adapted to the 450k array finding find differentially methylated regions DMR. 91 This tool is a version of the bump hunting algorithm (Andrew E Jaffe et al. 2012) adapted to the 450k array finding find differentially methylated regions DMR.
99 92
100 The output is an interval file with the following columns: 93 The output is an interval file with the following columns:
101 94
102 - seqnames 95 - chr
103 - start 96 - start
104 - end 97 - end
105 - width
106 - area
107 - value
108 98
109 ]]></help> 99 ]]></help>
110 <expand macro="citations" /> 100 <expand macro="citations" />
111 </tool> 101 </tool>