[R] reading table

Abi Ghanem josephine josephine.abighanem at ibpc.fr
Wed Jan 9 16:18:30 CET 2008


Hi,
I am encountering a problem in reading a file,
the file looks like that:
T  3  0       --       --     --    T     --       --     --     18.98
   3  1      6.75     4.39    39          --       --     --     18.58
   3  2      6.90     4.90    43          --       --     --     18.63
   3  3      7.07     5.39    48          --       --     --     18.78
G  4  0      7.41     5.54    47    G     --       --     --     18.90
   4  1      7.44     5.99    30        10.93     5.30    23     18.95
   4  2      7.27     6.05    23        11.16     5.74    19     18.96
   4  3      7.27     5.54    27        11.58     5.95    18     18.97
the first an the 7th column contains only T and G
my problem is i want to have the 4th column as a vector : 6.75, 6.90, 
7.07, 7.41, 7.44, 7.27, 7.27.

when i do a simple read.delim(data, sep="", header=FALSE), i get this

T  3     0    --    --     --     T     --    --  -- 18.98
3  1  6.75  4.39    39     --    --     -- 18.58
3  2  6.90  4.90    43     --    --     -- 18.63
3  3  7.07  5.39    48     --    --     -- 18.78
G  4     0  7.41  5.54     47     G     --    --  -- 18.90
4  1  7.44  5.99    30  10.93  5.30     23 18.95
4  2  7.27  6.05    23  11.16  5.74     19 18.96
4  3  7.27  5.54    27  11.58  5.95     18 18.97

with the first line containing T, 3, 3, 3, G, 4, 4, 4 so the values are 
shifted in the 1st and 5th row


i tried to change sep="" to sep="\t", but than i don't get a matrix
i just get a one column file.
"  T  3  0       --       --     --    T     --       --     --     18.98"
"     3  1      6.75     4.39    39          --       --     --     18.58"
"     3  2      6.90     4.90    43          --       --     --     18.63"
"     3  3      7.07     5.39    48          --       --     --     18.78"
"  G  4  0      7.41     5.54    47    G     --       --     --     18.90"
"     4  1      7.44     5.99    30        10.93     5.30    23     18.95"
"     4  2      7.27     6.05    23        11.16     5.74    19     18.96"
"     4  3      7.27     5.54    27        11.58     5.95    18     18.97"

My question is there is a way to read the file either with skipping the 
first column and the 7th,
Or how can i get to have a vector with the 4th column.

Thanks for the help,
Josephine

-- 


Josephine ABI GHANEM
IBPC, UPR 9080
13, rue P. et M. Curie,
75005 Paris, FRANCE

email: josephine.abighanem at ibpc.fr
tel: 01 58 41 51 67
      06 28 07 25 71




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