Were they assimilated into the natives, enslaved/raped, or were they just killed?
Specifically on the American Indians of the east coast of what was to be the United States there are cases of massacres as well as cases of assimilation. Generally many American Indian cultures emphasized capturing prisoners as an objective of war as opposed to killing. Men might be killed in massacres, but there are many cases of women and children being taken and assimilated into the culture of their captors, much in the same way that these groups would assimilate non-europeans captives. This became such a trope in early European American culture that it spawned some of the first uniquely American literature, Captivity Narratives, the most famous of which is Mary Rowlandson's "A Narrative of the Captivity and Restoration of Mrs. Mary Rowlandson".
These narratives give a pretty good insight into how captives were treated and assimilated. They were most definitely slaves in the sense that they were deprived of freedoms, but they weren't necessarily treated as property and full assimilation and acceptance was very possible. None of these early narratives describe rape, this might be because Puritan women would not want to discuss and publish such an experience, but I've also read some early accounts that suggest that rape was simply not a part of certain American Indian cultures in the same way that ritual cannibalism was something that was totally foreign to the Puritans.
There are still plenty of accounts of violence against men, women, and children. The Jamestown Massacre for example was indiscriminate on a large scale and this kind of violence played a large role in shaping European attitudes towards their Indian neighbors.
The last example would be the mysterious lost colony of Roanoke. The exact details of what happened to the Roanoke colony are lost to history. There have been many conflicting theories, some suggesting massacre and others assimilation. Archeological evidence as well as early accounts heavily support the idea that at least some europeans went inland and assimilated into the local Croatan society. Whether this assimilation included men and whether it was the result of violence is still very uncertain.