Question: > DBdata <-dba(sampleSheet = samples) Error: object of type 'closure' is not subsettable
0
gravatar for jason.williams
5 months ago by
jason.williams0 wrote:

Hi, I am using this vignette to guide me through differential ChIPSeq analysis - https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2018/ChIP/Practicals/Practical4differentialBindingDB.html

Using this sample sheet in a .csv file

    SampleID    Tissue  Factor  Condition   Treatment   Replicate   bamreads    Control ID  bamControl  Peaks   PeakCaller
1   C0011   PBMC_Cancer H3K4Me3 Resistant   Extreme_Phenotype   1   1_059D_00OLSwansea_CS001_H3K27Ac_hs_i85_trim_bowtie2UP(copy 1).bam  C0011c  3_059S_00OLSwansea_Input_hs_i87_trim_bowtie2UP.bam  CS_H3K27Ac_summits.bed  bed
2   C0012   PBMC_Cancer H3K4Me4 Resistant   Extreme_Phenotype   2   1_059D_00OLSwansea_CS001_H3K27Ac_hs_i85_trim_bowtie2UP.bam  C0011c  3_059S_00OLSwansea_Input_hs_i87_trim_bowtie2UP (copy 1).bam CS_H3K27Ac_summits(copy 1).bed  bed
3   Con0011 PBMC_Normal H3K4Me5 Normal  Non-extreme_Phenotype   1   C_ENCFF350ISY_H3K27Ac.bam   Con0011c    C_ENCFF380MFX_inp.bam   Con_H3K27Ac_summits.bed bed
4   Con0012 PBMC_Normal H3K4Me6 Normal  Non-extreme_Phenotype   2   C_ENCFF350ISY_H3K27Ac(copy 1).bam   Con0011c    C_ENCFF380MFX_inp(copy 1).bam   Con_H3K27Ac_summits(copy 1).bed bed

I followed the vignette using the following script:

# read csv of sample sheet into dataframe
samples <-read.csv(Extreme_Phenotype_H3K27Ac.csv)
samples
# Load and read the sample sheet
DBdata <-dba(sampleSheet = samples)

I get the following error in the console:

 DBdata <-dba(sampleSheet = samples)
Error: object of type 'closure' is not subsettable

I am new to using R so I apologise if I am making a silly mistake.

Thanks in advance,

Jason

diffbind R r studio • 123 views
ADD COMMENTlink modified 5 months ago by James W. MacDonald52k • written 5 months ago by jason.williams0
Answer: > DBdata <-dba(sampleSheet = samples) Error: object of type 'closure' is not sub
2
gravatar for James W. MacDonald
5 months ago by
United States
James W. MacDonald52k wrote:

The error you see is what you get when you try to subset a function:


> read.csv[1:3]
Error in read.csv[1:3] : object of type 'closure' is not subsettable

Which makes me think that your 'samples' object is actually a pointer to a function? I don't know, but do note that read.csv expects the first argument to be a quoted file name, and you are passing an R object (since it's unquoted). You can hypothetically do that sort of thing, like

Extreme_Phenotype_H3K27Ac.csv <- "Extreme_Phenotype_H3K27Ac.csv"
samples <- read.csv(Extreme_Phenotype_H3K27Ac.csv)

Which would work, but why would you do that? My best guess is that your samples object isn't a data.frame but is instead a function, and you need to fix something somewhere.

ADD COMMENTlink written 5 months ago by James W. MacDonald52k
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