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comparison rmarkdown_feature_counts.Rmd @ 0:5af86972b408 draft

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planemo upload
author mingchen0919
date Fri, 29 Dec 2017 15:03:18 -0500
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children a7f7e8a58a82
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1 ---
2 title: 'Feature Counts'
3 output:
4 html_document:
5 number_sections: true
6 toc: true
7 theme: cosmo
8 highlight: tango
9 ---
10
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
12 knitr::opts_chunk$set(
13 echo = opt$echo,
14 error = TRUE
15 )
16 ```
17
18
19 # User input
20
21 ```{r 'user input'}
22 opt
23 ```
24
25 # Calculate feature counts
26
27 ```{r 'ste[ 2'}
28 res = featureCounts(
29 files = strsplit(opt$input_bam_paths, ',')[[1]],
30 # annotation
31 annot.inbuilt=opt$annot_inbuilt,
32 annot.ext=opt$annot_ext,
33 isGTFAnnotationFile=opt$isGTFAnnotationFile,
34 GTF.featureType=opt$gtf_feature_type,
35 GTF.attrType=opt$gtf_attr_type,
36 chrAliases=opt$chr_aliases,
37
38 # level of summarization
39 useMetaFeatures=opt$use_meta_features,
40
41 # overlap between reads and features
42 allowMultiOverlap=opt$allow_multi_overlap,
43 minOverlap=opt$min_overlap,
44 largestOverlap=opt$largest_overlap,
45 readExtension5=opt$read_extension_5,
46 readExtension3=opt$read_extension_3,
47 read2pos=opt$read_2_pos,
48
49 # multi-mapping reads
50 countMultiMappingReads=opt$count_multi_mapping_reads,
51 fraction=opt$fraction,
52
53 # read filtering
54 minMQS=opt$min_mqs,
55 splitOnly=opt$split_only,
56 nonSplitOnly=opt$non_split_only,
57 primaryOnly=opt$primary_only,
58 ignoreDup=opt$ignore_dup,
59
60 # strandness
61 strandSpecific=opt$strand_specific,
62
63 # exon-exon junctions
64 juncCounts=opt$junc_counts,
65 genome=opt$genome,
66
67 # parameters specific to paired end reads
68 isPairedEnd=opt$is_paired_end,
69 requireBothEndsMapped=opt$require_both_ends_mapped,
70 checkFragLength=opt$check_frag_length,
71 minFragLength=opt$min_frag_length,
72 maxFragLength=opt$max_frag_length,
73 countChimericFragments=opt$count_chimeric_fragments,
74 autosort=opt$auto_sort,
75
76 # miscellaneous
77 nthreads=opt$n_threads,
78 maxMOp=opt$max_mop,
79 reportReads=opt$report_reads
80 )
81 ```
82
83 # Write counts into CSV file
84
85 ```{r}
86 colnames(res$counts) = strsplit(opt$input_bam_names, ',')[[1]]
87 # write count into csv file
88 write.table(res$counts, file = 'feature_counts.txt')
89 ```
90
91 Display the first 100 rows.
92
93 ```{r}
94 datatable(head(res$counts, 100))
95 ```
96
97 # Save results into RData file
98
99 ```{r}
100 save(res, file = 'feature_counts.RData')
101 str(res)
102 ```
103
104