changeset 10:1cff3a3e2b94 draft

working version

--- a/rmarkdown_feature_counts.Rmd	Thu Dec 28 23:33:30 2017 -0500
+++ b/rmarkdown_feature_counts.Rmd	Fri Dec 29 00:17:31 2017 -0500
@@ -23,7 +23,60 @@
 ```
 
 ```{r 'ste[ 2'}
+res = featureCounts(
+  files = strsplit(opt$input_bam, ',')[[1]],
+  # annotation
+	annot.inbuilt=opt$annot_inbuilt,
+	annot.ext=opt$annot_ext,
+	isGTFAnnotationFile=opt$isGTFAnnotationFile,
+	GTF.featureType=opt$gtf_feature_type,
+	GTF.attrType=opt$gtf_attr_type,
+	chrAliases=opt$chr_aliases,
+	
+	# level of summarization
+	useMetaFeatures=opt$use_meta_features,
+	
+	# overlap between reads and features
+	allowMultiOverlap=opt$allow_multi_overlap,
+	minOverlap=opt$min_overlap,
+	largestOverlap=opt$largest_overlap,
+	readExtension5=opt$read_extension_5,
+	readExtension3=opt$read_extension_3,
+	read2pos=opt$read_2_pos,
+	
+	# multi-mapping reads
+	countMultiMappingReads=opt$count_multi_mapping_reads,
+	fraction=opt$fraction,
 
+	# read filtering
+	minMQS=opt$min_mqs,
+	splitOnly=opt$split_only,
+	nonSplitOnly=opt$non_split_only,
+	primaryOnly=opt$primary_only,
+	ignoreDup=opt$ignore_dup,
+	
+	# strandness
+	strandSpecific=opt$strand_specific,
+	
+	# exon-exon junctions
+	juncCounts=opt$junc_counts,
+	genome=opt$genome,
+	
+	# parameters specific to paired end reads
+	isPairedEnd=opt$is_paired_end,
+	requireBothEndsMapped=opt$require_both_ends_mapped,
+	checkFragLength=opt$check_frag_length,
+	minFragLength=opt$min_frag_length,
+	maxFragLength=opt$max_frag_length,
+	countChimericFragments=opt$count_chimeric_fragments,	
+	autosort=opt$auto_sort,
+	
+	# miscellaneous
+	nthreads=opt$n_threads,
+	maxMOp=opt$max_mop,
+	reportReads=opt$report_reads
+)
+str(res)
 ```
 
 

--- a/rmarkdown_feature_counts_render.R	Thu Dec 28 23:33:30 2017 -0500
+++ b/rmarkdown_feature_counts_render.R	Fri Dec 29 00:17:31 2017 -0500
@@ -32,41 +32,41 @@
   #+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
   args_list=list()
   ##------- 1. input data ---------------------
-  args_list$ECHO = c('echo', 'e', '1', 'character')
+  args_list$e = c('echo', 'e', '1', 'logical')
   args_list$a = c('input_bam', 'a', '1', 'character')
-  args_list$b = c('annot_built', 'b', '1', 'character')
+  args_list$b = c('annot_inbuilt', 'b', '1', 'character')
   args_list$c = c('annot_ext', 'c', '1', 'character')
-  args_list$f = c('isGTFAnnotationFile', 'f', '1', 'character')
+  args_list$f = c('isGTFAnnotationFile', 'f', '1', 'logical')
   args_list$g = c('gtf_feature_type', 'g', '1', 'character')
   args_list$h = c('gtf_attr_type', 'h', '1', 'character')
   args_list$i = c('chr_aliases', 'i', '2', 'character')
-  args_list$j = c('use_meta_features', 'j', '1', 'character')
-  args_list$k = c('allow_multi_overlap', 'k', '1', 'character')
+  args_list$j = c('use_meta_features', 'j', '1', 'logical')
+  args_list$k = c('allow_multi_overlap', 'k', '1', 'logical')
   args_list$l = c('min_overlap', 'l', '1', 'integer')
-  args_list$m = c('largest_overlap', 'm', '1', 'character')
+  args_list$m = c('largest_overlap', 'm', '1', 'logical')
   args_list$n = c('read_extension_5', 'n', '1', 'integer')
   args_list$o = c('read_extension_3', 'o', '1', 'integer')
   args_list$p = c('read_2_pos', 'p', '1', 'character')
-  args_list$q = c('count_multi_mapping_reads', 'q', '1', 'character')
-  args_list$u = c('fraction', 'u', '1', 'character')
+  args_list$q = c('count_multi_mapping_reads', 'q', '1', 'logical')
+  args_list$u = c('fraction', 'u', '1', 'logical')
   args_list$v= c('min_mqs', 'v', '1', 'integer')
-  args_list$w= c('split_only', 'w', '1', 'character')
-  args_list$x= c('non_split_only', 'x', '1', 'character')
-  args_list$y= c('primary_only', 'y', '1', 'character')
-  args_list$z= c('ignore_dup', 'z', '1', 'character')
+  args_list$w= c('split_only', 'w', '1', 'logical')
+  args_list$x= c('non_split_only', 'x', '1', 'logical')
+  args_list$y= c('primary_only', 'y', '1', 'logical')
+  args_list$z= c('ignore_dup', 'z', '1', 'logical')
   args_list$A= c('strand_specific', 'A', '1', 'integer')
-  args_list$B= c('junc_counts', 'B', '1', 'character')
+  args_list$B= c('junc_counts', 'B', '1', 'logical')
   args_list$C= c('genome', 'C', '1', 'character')
-  args_list$D= c('is_paired_end', 'D', '1', 'character')
-  args_list$E= c('require_both_ends_mapped', 'E', '1', 'character')
-  args_list$F= c('check_frag_length', 'F', '1', 'character')
+  args_list$D= c('is_paired_end', 'D', '1', 'logical')
+  args_list$E= c('require_both_ends_mapped', 'E', '1', 'logical')
+  args_list$F= c('check_frag_length', 'F', '1', 'logical')
   args_list$G= c('min_frag_length', 'G', '1', 'integer')
   args_list$H= c('max_frag_length', 'H', '1', 'integer')
-  args_list$I= c('count_chimeric_fragments', 'I', '1', 'character')
-  args_list$J= c('auto_sort', 'J', '1', 'character')
+  args_list$I= c('count_chimeric_fragments', 'I', '1', 'logical')
+  args_list$J= c('auto_sort', 'J', '1', 'logical')
   args_list$K= c('n_threads', 'K', '1', 'integer')
   args_list$L= c('max_mop', 'L', '1', 'integer')
-  args_list$M= c('report_reads', 'M', '1', 'character')
+  args_list$M= c('report_reads', 'M', '1', 'logical')
   
   ##--------2. output report and outputs --------------
   args_list$REPORT_HTML = c('report_html', 'r', '1', 'character')