R read.table() saying line does not have correct number of elements - when I check, it definitely does

Question

[SpacemanSpiffo]

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

[ATpoint]

Can you provide the table up to that line for download?

[SpacemanSpiffo]

Yes, thanks for replying. I've amended my original post with a link to the download for the first 200 lines.

Answer 1

[h.mon]

Use read.csv():

t3 <- read.csv( "first200.csv" )

[SpacemanSpiffo]

Wow, that worked perfectly first try, thanks very much. Any idea why read.table() wasn't working? Normally specifying sep = "," works fine

[Martombo]

It seems that the hash on column 29 was causing read.table to stop reading the line. Could that be the case?

[h.mon]

Yes, this is exactly the case, the default for read.table() is comment.char = "#".

Answer 2

[ATpoint]

Another option using the data.table package, especially helpful when the file is large (hundreds of Mb or even Gb):

fread("your.file", sep=",", data.table=F)

Answer 3

[Chirag Parsania]

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>