I have some problems running my script with the latest version of ChIPQC1.12. The script was working well on the older version of the package. I was wondering if someone else is also facing the same problem and could give me a solution. Below is my code and output:
samples = read.csv("metadata.csv") mydata= ChIPQC(samples, annotation=NULL, chromosomes=NULL)
sample_0 sample_0 1 bed
sample_5 sample_5 1 bed
sample_10 sample_10 1 bed
sample_15 sample_15 1 bed
sample_20 sample_20 1 bed
Computing metrics for 5 samples...
Bam file has 5 contigs
Now it calculates histogram, SSD, unique positions, shift etc only for Chr1, Chr2 and Chr3.
I also tried giving all five chr as vectors: chromosomes= c("Chr1","Chr2","Chr3","Chr4","Chr5") but results are same.
Next I tried constructing annotation using genomic features. As follows:
axx_txdb= makeTxDbFromGFF(file="mygff_GFF3_genes_transposons.201606.gff", dataSource=my gff file", format="gff3", organism="unknown organism")
but including the annotation lead to another problem. I am very new to genomicfeatures package. Not sure if I am doing anything wrong here.
mychip= ChIPQC(samples, annotation=axx_txdb,chromosomes=NULL)
Error in GeneAnnotation == "hg19" :
comparison (1) is possible only for atomic and list types
Why it is considering "hg19" for annotation??
To add information re my metadata file. I have the following columns: