hierarchAnnot: hierarchAnnot

In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries

Description

Hierarchical annotation of the CAGE clusters

Usage

hierarchAnnot(annot)

Arguments

annot

A data frame with a feature column that contains comma-separated annotations, like for instance ‘exon,intron’. The annotation data frame is typically loaded from a file produces with commands such as the following. zcat /analysisdata/annotations/100712hg19/refGeneTssProximal500.bed.gz | awk '{OFS="\t"}{print $1, $2, $3, "promoter", $5, $6}' > 100712hg19.annot zcat /analysisdata/annotations/100712hg19/refGeneExon.bed.gz | awk '{OFS="\t"}{print $1, $2, $3, "exon", $5, $6}' >> 100712hg19.annot zcat /analysisdata/annotations/100712hg19/refGene.bed.gz | awk '{OFS="\t"}{print $1, $2, $3, "gene", $5, $6}' >> 100712hg19.annot zcat $LIBRARY.l1.gz | grep -v \# | sed 1d | awk '{OFS="\t"}{print $2, $3, $4, "l2", "1000", $5}' > $LIBRARY.l1.bed zcat $LIBRARY.l2.gz | grep -v \# | sed 1d | awk '{OFS="\t"}{print $2, $3, $4, "l2", "1000", $5}' > $LIBRARY.l2.bed bedtools intersect -a $LIBRARY.l1.bed -b 100712hg19.annot -s -loj | awk '{OFS="\t"}{print $1":"$2"-"$3$6,$10}' | bedtools groupby -g 1 -c 2 -o collapse > $LIBRARY.l1.annot bedtools intersect -a $LIBRARY.l2.bed -b 100712hg19.annot -s -loj | awk '{OFS="\t"}{print $1":"$2"-"$3$6,$10}' | bedtools groupby -g 1 -c 2 -o collapse > $LIBRARY.l2.annot

Details

Parse an annotation data frame and retains only one annotation, in the order ‘promoter’, ‘exon’, ‘intron’ and ‘unknown’.

Value

The annotation table with the hierarchical annotation in a column called class.

See Also

loadLogs

Other smallCAGEqc annotation functions: hannot, mapStats, plotAnnot, ranges2annot, ranges2genes

charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.