Changing values in a raster

I have a raster file (created in QGIS, from a vectorial file). I would like to know if it is possible, in R: 1) to change the values of the pixels? (I believe all the cells have the value "1" associated, or at least the blue pixels (check images below), and I don't know the values for the white pixels, but I would like to set it to "2", for instance, so it would be binary) 2) to "crop" the raster? Here are the characteristics of the input raster:

> catC1raster class : RasterLayer dimensions : 1384, 2359, 3264856 (nrow, ncol, ncell) resolution : 30, 30 (x, y) extent : 325352.8, 396122.8, 4613074, 4654594 (xmin, xmax, ymin, ymax) coord. ref. : +proj=utm +zone=31 +datum=WGS84 +units=m +no_defs +ellps=WGS84 +towgs84=0,0,0 names : CAT_C1_30m 

And here is the plot:

Yes. The raster package (cran.r-project.org/web/packages/raster/index.html) can modify the pixel values. Functions subs() and reclasify() are two ways to do it. The cunction crop() will crop your raster.

the crop function worked perfectly, thanks!! regarding the reclassify()/subs(), how can I find first the values each pixel has??

For each pixel my advise is to get them into a dataframe format with rasterToPoints(). Do note that depending on the size of your raster, the resulting dataframe might be very large.You could try values().