[R] Reading ASCII files

[Gabor Grothendieck]

Or assuming that you want snp_id to be character and other columns
to have their default class (i.e. ID is numeric, description is factor
and genotype is factor) and also assuming that 1st line, etc. is not 
actually part of the file:

read.table(myfilename, as.is = "snp_id", header = TRUE, fill = TRUE, 
   na.string = "")


Liaw, Andy <andy_liaw <at> merck.com> writes:

: 
: You can use fill=TRUE and na.string="" in read.table().  E.g.,
: 
: > try.dat <- read.table("clipboard", colClasses=rep("character", 6), 
: +                       header=TRUE, fill=TRUE, na.string="")
: > try.dat
:   X1st line    ID  description   snp_id genotype
: 1  2nd line 10003          Low rs152240     <NA>
: 2  3rd line 10003     Moderate rs189011       TC
: 3  4th line 10004 Conservative rs152240       GC
: 4  5th line 10004          Bad rs154354     <NA>
: 5  6th line 10013          Bad rs152240     <NA>
: 6  7th line 10019 Conservative rs152240       AC
: 
: HTH,
: Andy
: 
: > From: Cristian Pattaro
: > 
: > Dear all,
: > I need to read an ASCII file with diffent length lines.
: > 
: > This is what is contained in the file gene.txt:
: > 1st line  ID description snp_id genotype
: > 2nd line 10003 Low rs152240 
: > 3rd line 10003 Moderate rs189011 TC
: > 4th line 10004 Conservative rs152240 GC
: > 5th line 10004 Bad rs154354
: > 6th line 10013 Bad rs152240
: > 7th line 10019 Conservative rs152240 AC
: > etc...
: > 
: > This is what I would like to obtain in R:
: > ID        description         snp_id          genotype
: > 10003    Low                 rs152240     NA
: > 10003    Moderate         rs189011     TC
: > 10004    Conservative    rs152240     GC
: > 10004    Bad                  rs154354     NA
: > 10013    Bad                  rs152240     NA
: > 10019    Conservative    rs152240     AC
: > 
: > Read.table() doesn't work in these situations because of the 
: > irregular 
: > pattern of data. Have you got any suggestion?
: > Thanks a lot!
: > Cristian
: > 
: > ===========================================
: > Cristian Pattaro
: > ===========================================
: > 
: > Unit of Epidemiology & Medical Statistics
: > Department of Medicine and Public Health
: > University of Verona
: > cristian <at> biometria.univr.it
: > http://biometria.univr.it
: > ===========================================
: > 
: > 
: > 	[[alternative HTML version deleted]]
: > 
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: >
: 
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