CODEWITHSUNDEEP
r
tanu
tanu

Reputation: 3

Data frame tranformation to matrix with counts

I have a data file representing the presence of genes in respective strains like this:

|gene name| strains|

|BCAL0113| MS2140|

|BCAL0113| VC9970|

|BCAL0113| VC9872|

|BCAL0113| VC9842|

|BCAL0113| VC9789|

|BCAL0113| VC9670|

|BCAL0113| VC9612|

|BCAL0114| VC9444|

|BCAL0114| VC8412|

|BCAL0114| VC8319|

|BCAL0114| VC7880|

|BCAL0115| VC7879|

|BCAL0115| VC7723|

|BCAL0116| VC7722|

|BCAL0116| VC7718|

I want to create a matrix that shows gene_names as first column (column_names) and strains as first row (row_names) with counts as 1 or 0 for presence or absence respectively. i need matrix table like this:

     MS2140 VC9970  VC9872  VC9842  VC8319  VC7880  VC7879  VC7723

BCAL0113 1 1 1 1 0 0 0 0 0 0

BCAL0114 0 0 0 0 1 0 0 0 0 0

BCAL0115 0 0 0 0 0 1 1 0 0 0

BCAL0116 0 0 0 0 0 0 0 0 1 1

I want to create a matrix of the presence or absence of genes in respective strains.

Upvotes: 0

Views: 89

Answers (1)

ivan866
ivan866

Reputation: 582

m1 <- t(matrix(c('BCAL0113', 'MS2140', 'BCAL0113', 'VC9970', 'BCAL0113', 'VC9872', 'BCAL0113', 'VC9842', 'BCAL0113', 'VC9789', 'BCAL0113', 'VC9670', 'BCAL0113', 'VC9612', 'BCAL0114', 'VC9444', 'BCAL0114', 'VC8412', 'BCAL0114', 'VC8319', 'BCAL0114', 'VC7880', 'BCAL0115', 'VC7879', 'BCAL0115', 'VC7723', 'BCAL0116', 'VC7722', 'BCAL0116', 'VC7718'), nrow=2))
df <- as.data.frame(m1)
t1 <- table(df); t1

Upvotes: 1

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