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jokergoo / EnrichedHeatmap

make enriched heatmap which visualizes the enrichment of genomic signals to specific target regions.
http://jokergoo.github.io/EnrichedHeatmap/
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customer reference genes annotation #37

Closed skytguuu closed 5 years ago

skytguuu commented 5 years ago

Hi,

I tried to use enrichment heatmap to normalize chip-seq data. However, when I loaded my reference gene annotation (gtf file) downloaded from UCSC, then it repored an error. ################### the command is: normalizeToMatrix(k4me3,tss,value_column="Peak") ################## the error is: Error in (function (classes, fdef, mtable): unable to find an inherited method for function 'strand<-' for signature '"data.frame","character"'.

Could you give me some advises? Thanks for your help. Best, Garen

jokergoo commented 5 years ago

Can you show me the first several lines of k4me3 and tss?

skytguuu commented 5 years ago

Thanks for your promptly help. My first lines of k4me3 and tss are as followed: ##########

tss[1:2] GRanges object with 2 ranges and 2 metadata columns: seqnames ranges strand | tx_id tx_name

| [1] chr1 [4797974, 4797974] + | 1 uc007afg.1 [2] chr1 [4797974, 4797974] + | 2 uc007afh.1 ------- seqinfo: 35 sequences (1 circular) from mm9 genome k4me3[1:2] GRanges object with 2 ranges and 2 metadata columns: seqnames ranges strand | score peak | X0001 chr1 [4774089, 4776789] * | 1815 1288 X0002 chr1 [4797273, 4799175] * | 1455 378 ------- seqinfo: 15 sequences from an unspecified genome; no seqlengths ############ And now, I solved this problem because I did not use "toGRanges" to change the k4me3 input format. But now I am confused about the parameter of "value_column". Because I got the output from macs2, it is the narrowpeak file. Those columns are including "score" and "Peak". I was wondering which one (score or peak) is better to use to normalization?

Thanks

jokergoo commented 5 years ago

I normally use the fifth column in the bed file for the "narrowPeak" file because it is used for genomic track visualization and I assume they are kind like normalized values.

skytguuu commented 5 years ago

I am appreciated for your help.

Thanks, Best