|
0
|
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
|
