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