On 2020-03-30 21:43 -0500, Ana Marija wrote:
> I did run your workflow and this is what I got:
>
> > newout<-merge(output11.frq,marker_info[,c("V5","match_col")],by="match_col")
> Error in `[.data.frame`(marker_info, , c("V5", "match_col")) :
> undefined columns selected
>
> this is how marker-info looks like:
Hi Ana,
perhaps adding comment.char="#" as an argument to read.csv might
help?
Making the output11.frq$match_col column might perhaps be easier
using gsub, have a look:
marker_info <- "#Column Description:
#Column is separated by ','.
#Chr: Chromosome on NCBI reference genome.
#Pos: chromosome position when snp has unique hit on reference genome.
Otherwise this field is NULL.
#Submitter_snp_name: The string identifier of snp on the platform. This is
the dbSNP local_snp_id.
#Ss#: dbSNP submitted snp Id. Each snp sequence on the platform gets a unique
ss#.
#Rs#: refSNP cluster accession. Rs# for the dbSNP refSNP cluster that the
sequence for this ss# maps to.
#Genome_build_id: Genome build used to map the SNP (a string)
#ALLELE1_genome_orient: genome orientation allele1, same as which genotypes are
reported.
#ALLELE2_genome_orient: genome orientation allele2, same as which genotypes are
reported.
#ALLELE1_orig_assay_orient: original reported orientation for the SNP
assay, will correspond to CEL files and the ss_id.
#ALLELE2_orig_assay_orient: original reported orientation for the SNP
assay, will correspond to CEL files and the ss_id.
#QC_TYPE: A-autosomal and P-pseudo-autosomal; X: X-linked;
Y-Y-linked;NA-disable QC for this snp.
#SNP_flank_sequence: snp sequence on the reference genome orientation. 40bp
on each side of variation.
#SOURCE: Platform specific string identifying assay (e.g. HBA_CHIP)
#Ss2rs_orientation: ss to rs orientation. +: same; -: opposite strand.
#Rs2genome_orienation: Orientation of rs flanking sequence to reference
genome. +: same orientation, -: opposite.
#Orien_flipped_assay_to_genome: y/n: this column would be the value of the
exclusive OR from ss2rs_orientation XOR rs2genome_orientation.
#Probe_id: NCBI probe_id.
#neighbor_snp_list: List of neighbor snp and position within 40kb
up/downstream.
#dbSNP_build_id: dbSNP build id.
#study_id: unique id with prefix: phs.
#
#
Chr,Pos,Submitter_snp_name,Ss#,Rs#,Genome_build_id,ALLELE1_genome_orient,ALLELE2_genome_orient,ALLELE1_orig_assay_orient,ALLELE2_orig_assay_orient,QC_TYPE,SNP_flank_sequence,SOURCE,Ss2rs_orientation,Rs2genome_orienation,Orien_flipped_assay_to_genome,Probe_id,neighbor_snp_list,dbSNP_build_id,study_id
1,742429,SNP_A-1909444,ss66079302,rs3094315,36.2,G,A,C,T,A,GCACAGCAAGAGAAAC[A/G]TTTGACAGAGAATACA,Sty,+,-,y,,,127,phs000018
1,769185,SNP_A-4303947,ss66273559,rs4040617,36.2,A,G,A,G,A,GCTGTGAGAGAGAACA[A/G]TGTCCCAATTTTGCCC,Sty,+,+,n,,,127,phs000018
1,775852,SNP_A-1886933,ss66317030,rs2980300,36.2,T,C,A,G,A,GAATGACTGTGTCTCT[C/T]TGAGTTAGTGAAGTCA,Nsp,-,+,y,,,127,phs000018
"
marker_info <-
read.csv(text=marker_info,
header=FALSE,
stringsAsFactors=FALSE,
comment.char="#")
output11.frq <-
"CHR SNP A1 A2 MAF NCHROBS
1 1:775852:T:C T C 0.1707 3444
1 1:1120590:A:C C A 0.08753 3496
1 1:1145994:T:C C T 0.1765 3496
1 1:1148494:A:G A G 0.1059 3464
1 1:1201155:C:T T C 0.07923 3496"
output11.frq <-
read.table(text=output11.frq, header=TRUE,
stringsAsFactors=FALSE)
output11.frq$match_col <-
gsub("^([0-9]+):([0-9]+).*", "\\1:\\2",
output11.frq$SNP)
marker_info$match_col <-
apply(marker_info[,1:2], 1, paste,
collapse=":")
merge(x=output11.frq,
y=marker_info[,c("V5", "match_col")],
by="match_col")
Regards,
Rasmus
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