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NWPU-903PR / DMDeepm6A1.0

A R package used to identify single base resolution m6A and differential m6A methylation site from MeRIP-seq data version 1.0.
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Will not run examples. Tried in R version 3.6.3 and 3.6.1 #2

Open edf5 opened 3 years ago

edf5 commented 3 years ago

ip_bam1 <- system.file("extdata", "treated_ip1.bam", package="DMDeepm6A")
ip_bam2 <- system.file("extdata", "treated_ip2.bam", package="DMDeepm6A")
ip_bam3 <- system.file("extdata", "untreated_ip1.bam", package="DMDeepm6A")
ip_bam4 <- system.file("extdata", "untreated_ip2.bam", package="DMDeepm6A")
input_bam1 <- system.file("extdata", "treated_input1.bam", package="DMDeepm6A")
input_bam2 <- system.file("extdata", "treated_input2.bam", package="DMDeepm6A")
input_bam3 <- system.file("extdata", "untreated_input1.bam", package="DMDeepm6A")
input_bam4 <- system.file("extdata", "untreated_input2.bam", package="DMDeepm6A")

ip_bams <- c(ip_bam1, ip_bam2, ip_bam3, ip_bam4)
input_bams <- c(input_bam1, input_bam2, input_bam3, input_bam4)
sample_condition <- c("treated", "treated", "untreated", "untreated") gft_genome <- system.file("extdata", "genes.gtf", package="DMDeepm6A")

re <- dmdeepm6A(ip_bams = ip_bams,
input_bams = input_bams,
sample_conditions = sample_condition,
gft_genome = gft_genome)
Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK [1] "making transcriptome, this may take several minutes..." 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns [1] "Divide transcriptome into chr-gene-batch sections ..." [1] "Get Reads Count ..." [1] "This step may take a few hours ..." [1] "9.09 %" [1] "18.2 %" [1] "27.3 %" [1] "36.4 %" [1] "45.5 %" [1] "54.5 %" [1] "63.6 %" [1] "72.7 %" [1] "81.8 %" [1] "90.9 %" [1] "100 %" Error in if (ID[1] == TRUE) { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In is.na(PARAMETERS$TXDB) : is.na() applied to non-(list or vector) of type 'S4' 2: In is.na(PARAMETERS$TXDB) : is.na() applied to non-(list or vector) of type 'S4' 3: In is.na(PARAMETERS$TXDB) : is.na() applied to non-(list or vector) of type 'S4' 4: In is.na(PARAMETERS$TXDB) : is.na() applied to non-(list or vector) of type 'S4'

NWPU-903PR commented 2 years ago

This is an error caused by exomepeak, the reason should be the chrom names of toy bams are not the same as that version of txdb. I have updated the package and installation instruction, and the package is tested in R4.1.