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Hello,

I am attempting to run cinaR with this code. I have 20 samples, composed of 2 replicates of 10.
results <- cinaR(consensus_matrix, contrasts, reference.genome = "mm10", additional.covariates = c(rep("H", 5), rep("L", 5), rep("H", 5), rep("L", 5)), batch.correction = T, batch.information = c(rep(0, 10), rep(1,10)))

I have given this as contrasts:
contrasts<- c("H0", "H2", "H24", "H48", "H72", "L0", "L2", "L24", "L48", "L72","H0", "H2", "H24", "H48", "H72", "L0", "L2", "L24", "L48", "L72")

head(consensus_matrix) shows the below (only the fifrst 3 samples shown)

  chr   start     end Hi_0_REP1.mLb.clN.sorted.bam Hi_2_REP1.mLb.clN.sorted.bam Hi_24_REP1.mLb.clN.sorted.bam
1 chr1 3008684 3009119                            8                           12                             1
2 chr1 3012311 3012785                            8                            3                             1
3 chr1 3037464 3037989                            7                           20                             0
4 chr1 3046437 3046652                            6                            4                             0
5 chr1 3049581 3049922                            8                            4                             0
6 chr1 3053849 3054004                            0                           10                             0

dim(consensus_matrix)
[1] 312759 23

The traceback of the code shows:

Error in .get_data_frame_col_as_numeric(df, granges_cols[["start"]]) : some values in the "Start" column cannot be turned into numeric values
8. stop(wmsg("some values in the ", "\"", names(df)[[col]], "\" ", "column cannot be turned into numeric values"))
7. .get_data_frame_col_as_numeric(df, granges_cols[["start"]])
6. makeGRangesFromDataFrame(from, keep.extra.columns = TRUE)
5. asMethod(object)
4. as(seqnames, "GRanges")
3. GenomicRanges::GRanges(bed)
2. annotatePeaks(cp.filtered, reference.genome = reference.genome, show.annotation.pie = show.annotation.pie, verbose = verbose)
1. cinaR(consensus_matrix, contrasts, reference.genome = "mm10", additional.covariates = c(rep("H", 5), rep("L", 5), rep("H", 5), rep("L", 5)), batch.correction = T, batch.information = c(rep(0, 10), rep(1, 10)))

I've checked that the start and end columns contain only numeric values and no NAs. I'd appreciate any advice.

Thank you

If you have;

contrasts <- c("Severe", "Mild", "Healthy")

Then comparisons becomes Severe_Mild, Severe_Healthy, Mild_Healthy.

Hint: Take unique of the contrasts.

hello there,
cinaR is a wonderful tools for analysis ATAC-seq
I was wondering what is format of final.matrix (Annotated Consensus peaks)
I was trying to conducting Differential Analyses in my custom peak matrix with custom annotation
and I want to conduct Differential Analyses only rather than cinaR
much appreciated if you can provide any information

If there are any DA peaks it throws an error, fix it!

When run_enrichment is run with the GSEA as the enrichment method, the following error is given:

Error in fgsea::fgsea(pathways = geneset, stats = genes, eps = 0, minSize = 15, : unused argument (eps = 0)

The new version of fgsea::fgsea does not have the eps as an option.

if(verbose){
    # print message
}

Note: don't forget chIpSeeker.