Using this input (varible name changed from you question as using a variable named "matrix" can be confusing:
library(tm)
data("crude")
tdm <- TermDocumentMatrix(crude,control=list(removePunctuation = TRUE,
stopwords=TRUE))
Then this will avoid printing to screen
m <- as.matrix(tdm)
and then I would personally do something like
require(data.table)
data.table(m, keep.rownames=TRUE)
# rn 127 144 191 194 211 236 237 242 246 248 273 349 352 353 368 489 502 543 704 708
# 1: 100000 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
# 2: 108 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
# 3: 111 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
# 4: 115 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
# 5: 12217 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
# ---
# 996: yesterday 0 0 0 0 0 0 0 3 0 0 1 0 0 0 0 0 0 0 0 0
# 997: yesterdays 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
# 998: york 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0
# 999: zero 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0
# 1000: zone 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 0