I'm trying to read a csv table into R, but I get the following error "line 195 did not have 31 elements" however, when I check , both in Python and through copying the line into R as a string, the line (and the surrounding lines) definitely all have 31 elements.
Is anyone able to hazard a guess as to why R is flagging an incorrect number of lines?
Below is the line that is causing it to crash - supposed to have 31 elements, comma delimited
135411,single nucleotide variant,NM_001129727.2(PLEKHG4):c.1574A>G (p.Asp525Gly),25894,PLEKHG4,HGNC:24501,Likely benign,0,-,8044843,-,RCV000117986,MedGen:CN169374,not specified,germline,germline,GRCh37,NC_000016.9,16,67318242,67318242,A,G,16q22.1,no assertion criteria provided,1,,N,UniProtKB (protein):Q58EX7#VAR_050510,2,129965
The code I am using is:
t2 <- read.table("/Users/NAME/Desktop/variant_summary.csv", sep = ",")
Download link for first 200 lines of the csv file: https://drive.google.com/file/d/1_iUeGkyQwPvm3K2B5kfakhneuvpXpPYg/view?usp=sharing
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SpacemanSpiffo •
Wow, that worked perfectly first try, thanks very much. Any idea why read.table() wasn't working? Normally specifying sep = "," works fine
Tidy way
library(tidyverse)
dd <- read_delim("~/Downloads/first200.csv" , delim = ",")
dd
> dd
# A tibble: 199 x 31
`#AlleleID` Type Name GeneID GeneSymbol HGNC_ID ClinicalSignifi~ ClinSigSimple LastEvaluated `RS# (dbSNP)` `nsv/esv (dbVar~ RCVaccession PhenotypeIDS
<int> <chr> <chr> <int> <chr> <chr> <chr> <int> <chr> <int> <chr> <chr> <chr>
1 15041 indel NM_0~ 9907 AP5Z1 HGNC:2~ Pathogenic 1 29-Jun-10 397704705 - RCV000000012 MedGen:C315~
2 15041 indel NM_0~ 9907 AP5Z1 HGNC:2~ Pathogenic 1 29-Jun-10 397704705 - RCV000000012 MedGen:C315~
3 15042 dele~ NM_0~ 9907 AP5Z1 HGNC:2~ Pathogenic 1 29-Jun-10 397704709 - RCV000000013 MedGen:C315~
4 15042 dele~ NM_0~ 9907 AP5Z1 HGNC:2~ Pathogenic 1 29-Jun-10 397704709 - RCV000000013 MedGen:C315~
5 15043 sing~ NM_0~ 9640 ZNF592 HGNC:2~ Uncertain signi~ 0 29-Jun-15 150829393 - RCV000000014 MedGen:CN03~
6 15043 sing~ NM_0~ 9640 ZNF592 HGNC:2~ Uncertain signi~ 0 29-Jun-15 150829393 - RCV000000014 MedGen:CN03~
7 15044 sing~ NM_0~ 55572 FOXRED1 HGNC:2~ Pathogenic 1 7-Dec-17 267606829 - RCV00000001~ MedGen:C183~
8 15044 sing~ NM_0~ 55572 FOXRED1 HGNC:2~ Pathogenic 1 7-Dec-17 267606829 - RCV00000001~ MedGen:C183~
9 15045 sing~ NM_0~ 55572 FOXRED1 HGNC:2~ Pathogenic 1 1-Oct-10 267606830 - RCV000000016 MedGen:C183~
10 15045 sing~ NM_0~ 55572 FOXRED1 HGNC:2~ Pathogenic 1 1-Oct-10 267606830 - RCV000000016 MedGen:C183~
# ... with 189 more rows, and 18 more variables: PhenotypeList <chr>, Origin <chr>, OriginSimple <chr>, Assembly <chr>, ChromosomeAccession <chr>,
# Chromosome <chr>, Start <int>, Stop <int>, ReferenceAllele <chr>, AlternateAllele <chr>, Cytogenetic <chr>, ReviewStatus <chr>, NumberSubmitters <int>,
# Guidelines <chr>, TestedInGTR <chr>, OtherIDs <chr>, SubmitterCategories <int>, VariationID <int>
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Can you provide the table up to that line for download?
Yes, thanks for replying. I've amended my original post with a link to the download for the first 200 lines.
According to the way it is displayed in excel, your file should have 26 columns, not 31. Is it correct?
It should have 31 I believe - just double checked and in my Excel, 31 columns are displayed when I open "first200.csv"
You're right, I don't know why mine wasn't displaying all of them