eonurk / cinar Goto Github PK

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(verbose){
    # print message
}

Note: don't forget chIpSeeker.

If you have;

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

Then comparisons becomes Severe_Mild, Severe_Healthy, Mild_Healthy.

Hint: Take unique of the contrasts.

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

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